All File Changes
v266_preview to v266_preview2 (2012-04-10 to 2012-04-17) v266
- .gitignore
- lines changed 1, context: html, text, full: html, text
Adding python compiled files to ignore.
- python/lib/setup.py
- lines changed 23, context: html, text, full: html, text
Fixed setup.py to deal find and load submodules.
- python/lib/ucscgenomics/cv.py
- lines changed 4, context: html, text, full: html, text
removed CRLF from encode and fixed a small error in cv.py
- python/lib/ucscgenomics/encode.py
- lines changed 0, context: html, text, full: html, text
removed CRLF from encode and fixed a small error in cv.py
- src/cdnaAli/ali2alx/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/cdnaAli/binGood/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/cdnaAli/cdnaOff/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/cdnaAli/cluster/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/cdnaAli/findCdna/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/cdnaAli/g2cCheck/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/cdnaAli/introns/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/cdnaAli/sortFilt/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/cdnaAli/stitchea/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/getgene/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/hg/autoXml/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/hg/ctgToChromFa/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt2.daf
- lines changed 68, context: html, text, full: html, text
new daf file with new compositePrefix
- lines changed 68, context: html, text, full: html, text
this is replaced back by xxxProtGenc.daf as C & V are concerned that 2 may confuse people
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProtGenc.daf
- lines changed 68, context: html, text, full: html, text
for the new track for new datasets with hg19/gencode search and both unmodified and modified peptide mapping, this sharet the same supertrack with the old release
- lines changed 68, context: html, text, full: html, text
remove this file, it is replaced by xxxProt2.daf at the lab's request
- lines changed 68, context: html, text, full: html, text
changed the name back as C & V are concerned that 2 in xxxProt2 may confuse people
- src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechRnaSeq.daf
- lines changed 6, context: html, text, full: html, text
add Signal view for unique reads only bigwig file, named as xxx.unique.bigwig and use RawSignal view for the regular bigwig file containing both multi- and uniq-reads
- src/hg/encode/autoSql/README
- lines changed 3, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- src/hg/encode/autoSql/bedLogR.as
- lines changed 1, context: html, text, full: html, text
fixing bedLogR field definition
- lines changed 14, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- src/hg/encode/autoSql/bedLogR.sql
- lines changed 22, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- src/hg/encode/autoSql/bedRnaElements.as
- lines changed 13, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- src/hg/encode/autoSql/bedRnaElements.sql
- lines changed 20, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- src/hg/encode/autoSql/bedRrbs.as
- lines changed 15, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- src/hg/encode/autoSql/bedRrbs.sql
- lines changed 23, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 202, context: html, text, full: html, text
DEPRECATING OLD FORMATS1) Changed the order of formatChecker to group like with like
2) Changed wig and bedGraph validation to say submit as a bigWig
3) Changed fasta to say submit as a fastQ
4) Dropped peptideMapping and rpkm as one was a freepass and the other was an ill defined special case format for Caltech
5) Dropped PSL as we don't accept it, but kept code so that we could have it on file.
6) Changed tagAlign and pairedTagAligh to say submit as BAM
7) I also kept the bedGraph validator as example code in the comments, not sure if we need it
8) I left bedFloat and csqual and csfasta as I do not have clear directive.
- lines changed 16, context: html, text, full: html, text
removed support for quick option for encodeValidate
- src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCaltechRnaSeq.hg18.soft
- lines changed 1712, context: html, text, full: html, text
moved to downloads dir, these shouldnt be in the tree
- src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlLongRnaSeq.hg18.soft
- lines changed 111, context: html, text, full: html, text
moved to downloads dir, these shouldnt be in the tree
- src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlShortRnaSeq.hg18.soft
- lines changed 339, context: html, text, full: html, text
moved to downloads dir, these shouldnt be in the tree
- src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlShortRnaSeq.hg19.soft
- lines changed 407, context: html, text, full: html, text
moved to downloads dir, these shouldnt be in the tree
- src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeUwChIPSeq.hg18.soft
- lines changed 4436, context: html, text, full: html, text
moved to downloads dir, these shouldnt be in the tree
- src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeUwDgf.hg19.soft
- lines changed 448, context: html, text, full: html, text
moved to downloads dir, these shouldnt be in the tree
- src/hg/encode/hgEncodeApi/hgEncodeApi.c
- lines changed 264, context: html, text, full: html, text
Factor out ENCODE-specific API calls into separate CGI. Basic/rough cut
- lines changed 46, context: html, text, full: html, text
hgEncodeApi cleanup - retire encodeExpId request. Merge functionality into experiments request (it now filters on db= parameter)
- lines changed 189, context: html, text, full: html, text
hgEncodeApi and hgApi cleanup complete
- src/hg/encode/hgEncodeApi/makefile
- lines changed 14, context: html, text, full: html, text
Factor out ENCODE-specific API calls into separate CGI. Basic/rough cut
- src/hg/encode/makefile
- lines changed 2, context: html, text, full: html, text
hgEncodeApi cleanup - retire encodeExpId request. Merge functionality into experiments request (it now filters on db= parameter)
- src/hg/encode/validateFiles/README
- lines changed 18, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/expected/bam1.out
- lines changed 1, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/expected/bed12ok.out
- lines changed 1, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/expected/bigWig1.out
- lines changed 1, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/expected/bigWigTruncated.out
- lines changed 2, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/expected/tagAlign1.out
- lines changed 6, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/expected/tagAlign2.out
- lines changed 6, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/hg18_chromInfo.txt
- lines changed 49, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/bam1.bam
- lines changed 0, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/bed12.as
- lines changed 17, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/bed12bad.txt
- lines changed 69, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/bed12ok.txt
- lines changed 10, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/bed6bad.txt
- lines changed 15, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/bigWig1.bw
- lines changed 0, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/bigWigTruncated.bw
- lines changed 0, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/gnfAtlas2.bed15
- lines changed 10, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/hg18_chromInfo.txt
- lines changed 49, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/hg19_chromInfo.txt
- lines changed 93, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/hugechrom1.txt
- lines changed 1, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/tagAlign1.txt
- lines changed 1, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/input/tagAlign2.txt
- lines changed 1, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/makefile
- lines changed 16, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/tests/goodFemaleHg18.gappedPeak
- lines changed 13, context: html, text, full: html, text
Adding and improving test cases
- src/hg/encode/validateFiles/tests/goodFemaleHg19.bed10
- lines changed 34, context: html, text, full: html, text
Adding and improving test cases
- src/hg/encode/validateFiles/tests/goodFemaleHg19.bed11
- lines changed 35, context: html, text, full: html, text
Adding and improving test cases
- src/hg/encode/validateFiles/tests/goodFemaleHg19.bed12
- lines changed 35, context: html, text, full: html, text
Adding and improving test cases
- src/hg/encode/validateFiles/tests/goodFemaleHg19.narrowPeak
- src/hg/encode/validateFiles/tests/goodHg18.fasta
- lines changed 50, context: html, text, full: html, text
Adding and improving test cases
- src/hg/encode/validateFiles/tests/goodHg19.csfasta
- lines changed 49, context: html, text, full: html, text
Adding and improving test cases
- src/hg/encode/validateFiles/tests/goodHg19.csqual
- lines changed 49, context: html, text, full: html, text
Adding and improving test cases
- src/hg/encode/validateFiles/tests/goodHg19.fastq
- src/hg/encode/validateFiles/tests/goodMaleHg18.bedGraph
- src/hg/encode/validateFiles/tests/goodMaleHg18.pairedTagAlign
- src/hg/encode/validateFiles/tests/goodMaleHg18.tagAlign
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed3
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed4
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed5
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed6
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed7
- lines changed 141884, context: html, text, full: html, text
Adding more test files
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed8
- lines changed 141885, context: html, text, full: html, text
Adding more test files
- lines changed 3, context: html, text, full: html, text
Adding and improving test cases
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed9
- lines changed 141886, context: html, text, full: html, text
Adding more test files
- lines changed 3, context: html, text, full: html, text
Adding and improving test cases
- src/hg/encode/validateFiles/tests/goodMaleHg19.bedRrbs
- lines changed 141887, context: html, text, full: html, text
Adding more test files
- lines changed 5, context: html, text, full: html, text
Adding and improving test cases
- src/hg/encode/validateFiles/tests/goodMaleHg19.broadPeak
- lines changed 1, context: html, text, full: html, text
Removed an extra tab and the zero length line
- src/hg/encode/validateFiles/tests/goodMaleHg19.broadPeak.gz
- src/hg/encode/validateFiles/tests/goodMalehg19.bedRnaElements
- lines changed 624500, context: html, text, full: html, text
Start of a test suite
- src/hg/encode/validateFiles/tests/goodNoGenderHg19.bed15
- lines changed 40, context: html, text, full: html, text
Adding and improving test cases
- src/hg/encode/validateFiles/tests/goodNoGenderHg19.bedLogR
- src/hg/encode/validateFiles/tests/test1.right.txt
- lines changed 6, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/tests/test1.txt
- lines changed 1, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/tests/test2.right.txt
- lines changed 6, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/tests/test2.txt
- lines changed 1, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/tests/test3.bam
- lines changed 0, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/tests/test3.right.txt
- lines changed 0, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/tests/test4.bw
- lines changed 0, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/tests/test4.right.txt
- lines changed 0, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/validateFiles.c
- lines changed 567, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/encode/validateFiles/validateFilesUsage
- lines changed 30, context: html, text, full: html, text
Ever improving usage statement
- src/hg/fakeOut/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/hg/gbGetEntries/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/hg/gbOneAcc/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/hg/geneBounds/orf/orf.c
- lines changed 16, context: html, text, full: html, text
Changed name of function to avoid conflicting with lib function
- src/hg/hgApi/hgApi.c
- lines changed 195, context: html, text, full: html, text
hgEncodeApi and hgApi cleanup complete
- src/hg/hgGene/hgGeneData/Human/links.ra
- lines changed 1, context: html, text, full: html, text
Changed URL that Gepis Tissue points to (redmine #7251)
- src/hg/hgGene/hgGeneData/Mouse/links.ra
- lines changed 1, context: html, text, full: html, text
Changed URL that Gepis Tissue points to (redmine #7251)
- src/hg/hgGene/hgGeneData/Rat/rn4/links.ra
- lines changed 1, context: html, text, full: html, text
Changed URL that Gepis Tissue points to (redmine #7251)
- src/hg/hgGene/hgGeneData/links.ra
- lines changed 1, context: html, text, full: html, text
Changed URL that Gepis Tissue points to (redmine #7251)
- src/hg/hgTracks/hgTracks.c
- lines changed 1, context: html, text, full: html, text
restore code that adds oligoMatch track to trackDb (which was apparently accidently deleted in 0513e85cc01843ecc411b86dfce9180a8d1acf37) - fixes #7610
- src/hg/hgTracks/simpleTracks.c
- lines changed 18, context: html, text, full: html, text
removed some code criticized by hiram because it s special case handling with startswith and stringIn. still leave in the special case for Marker tracks because we will get many of them and having one rule per marker track will be very ugly. cannot do wildcard hash lookup myself, needs work in lookupTrack and also needs a wildcard-aware hash lookup function which I am not sure how to write
- lines changed 5, context: html, text, full: html, text
fixed indentation after larrym comments
- lines changed 9, context: html, text, full: html, text
going back to initial state
- lines changed 15, context: html, text, full: html, text
reverting previous 3 commits, cannot get it to work and fullfill hirams comments, added comments to explain why
- lines changed 2, context: html, text, full: html, text
commiting files again, hopefully have not messed up my git
- src/hg/hgc/pubs.c
- lines changed 52, context: html, text, full: html, text
html changed according to gregs corrections, suppress copyright notice for non-elsevier papers, suppress document type for publishers that have only one type (main text) (comment from larrym), many many indentation corrections to better comply to jim kent source style (larrym comments)
- lines changed 1, context: html, text, full: html, text
html modif suggested by greg
- src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
- lines changed 1, context: html, text, full: html, text
1. Change handling of hovering over experiments to suppress highlighting on IE which is too slow. Item *28 in redmine #5149. 2. Change handling of title (tooltip) on experiments for less overhead (assign as attribute, instead of dynamically generating on click)
- src/hg/htdocs/ENCODE/otherTerms.html
- lines changed 2, context: html, text, full: html, text
fixing the mouse strains tag so that it matches the tag used in track search and file search links back to this page, redmine 7100 note 31
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 7, context: html, text, full: html, text
In the BED detail example, combined the track line into a single line and inserted html tab codes in place of spaces. Fixed the error when copying and pasting the example as a custom track (redmine #7605).
- lines changed 2, context: html, text, full: html, text
Removed sentence about there being a line break in the track line since it no longer applied (redmine #7605)
- src/hg/inc/api.h
- lines changed 7, context: html, text, full: html, text
Minimal lib for shared functions for API programs
- src/hg/inc/chromInfo.h
- lines changed 5, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/inc/cv.h
- lines changed 11, context: html, text, full: html, text
hgEncodeApi and hgApi cleanup complete
- src/hg/inc/encode/encodeExp.h
- lines changed 3, context: html, text, full: html, text
hgEncodeApi cleanup - retire encodeExpId request. Merge functionality into experiments request (it now filters on db= parameter)
- lines changed 5, context: html, text, full: html, text
hgEncodeApi and hgApi cleanup complete
- src/hg/inc/encode/wgEncodeGencodeExonSupport.h
- src/hg/inc/gpFx.h
- lines changed 10, context: html, text, full: html, text
interim check-in for #6152. Adding variant structure and setup that allows maintaing multiple variants in one gp.
- lines changed 19, context: html, text, full: html, text
on-going work on annoGrator (#6152). Started using Sequence Ontology numbers from EBI, and added a generic variant structure as input to gpFx library
- src/hg/inc/soterm.h
- lines changed 62, context: html, text, full: html, text
on-going work on annoGrator (#6152). Started using Sequence Ontology numbers from EBI, and added a generic variant structure as input to gpFx library
- src/hg/inc/variant.h
- lines changed 26, context: html, text, full: html, text
interim check-in for #6152. Adding variant structure and setup that allows maintaing multiple variants in one gp.
- lines changed 5, context: html, text, full: html, text
on-going work on annoGrator (#6152). Started using Sequence Ontology numbers from EBI, and added a generic variant structure as input to gpFx library
- src/hg/js/encodeChipMatrix.js
- lines changed 13, context: html, text, full: html, text
hgEncodeApi cleanup - retire encodeExpId request. Merge functionality into experiments request (it now filters on db= parameter)
- lines changed 7, context: html, text, full: html, text
1. Change handling of hovering over experiments to suppress highlighting on IE which is too slow. Item *28 in redmine #5149. 2. Change handling of title (tooltip) on experiments for less overhead (assign as attribute, instead of dynamically generating on click)
- src/hg/js/encodeDataMatrix.js
- lines changed 14, context: html, text, full: html, text
hgEncodeApi cleanup - retire encodeExpId request. Merge functionality into experiments request (it now filters on db= parameter)
- lines changed 11, context: html, text, full: html, text
1. Change handling of hovering over experiments to suppress highlighting on IE which is too slow. Item *28 in redmine #5149. 2. Change handling of title (tooltip) on experiments for less overhead (assign as attribute, instead of dynamically generating on click)
- src/hg/js/encodeDataSummary.js
- lines changed 12, context: html, text, full: html, text
hgEncodeApi cleanup - retire encodeExpId request. Merge functionality into experiments request (it now filters on db= parameter)
- src/hg/js/encodeMatrix.js
- lines changed 17, context: html, text, full: html, text
1. Change handling of hovering over experiments to suppress highlighting on IE which is too slow. Item *28 in redmine #5149. 2. Change handling of title (tooltip) on experiments for less overhead (assign as attribute, instead of dynamically generating on click)
- src/hg/js/encodeProject.js
- lines changed 3, context: html, text, full: html, text
Factor out ENCODE-specific API calls into separate CGI. Basic/rough cut
- lines changed 12, context: html, text, full: html, text
hgEncodeApi cleanup - retire encodeExpId request. Merge functionality into experiments request (it now filters on db= parameter)
- src/hg/js/utils.js
- lines changed 2, context: html, text, full: html, text
Removed Regions link in File Search. Redmine #7005.
- src/hg/lib/annoGrateWig.c
- lines changed 6, context: html, text, full: html, text
Bugfix for #6152: forgot a sizeof when calling needMoreMem for array. Hurray for valgrind!
- src/hg/lib/annoGratorGpVar.c
- lines changed 6, context: html, text, full: html, text
interim check-in for #6152. Adding variant structure and setup that allows maintaing multiple variants in one gp.
- lines changed 1, context: html, text, full: html, text
oops... add parameters to gpFx routine
- lines changed 58, context: html, text, full: html, text
on-going work on annoGrator (#6152). Started using Sequence Ontology numbers from EBI, and added a generic variant structure as input to gpFx library
- src/hg/lib/annoStreamDb.c
- lines changed 1, context: html, text, full: html, text
Switching from sqlStoreResult back to sqlGetResult -- it's faster forgiant queries e.g. on snp135. For #6152
- src/hg/lib/api.c
- lines changed 32, context: html, text, full: html, text
Minimal lib for shared functions for API programs
- src/hg/lib/chromInfo.c
- lines changed 70, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/lib/customFactory.c
- lines changed 40, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/lib/cv.c
- lines changed 69, context: html, text, full: html, text
hgEncodeApi and hgApi cleanup complete
- src/hg/lib/encode/bedLogR.as
- lines changed 14, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- lines changed 4, context: html, text, full: html, text
First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
- src/hg/lib/encode/bedLogR.sql
- lines changed 22, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- src/hg/lib/encode/bedRnaElements.as
- lines changed 13, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- lines changed 5, context: html, text, full: html, text
First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
- src/hg/lib/encode/bedRnaElements.sql
- lines changed 20, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- src/hg/lib/encode/bedRrbs.as
- lines changed 15, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- lines changed 4, context: html, text, full: html, text
First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
- src/hg/lib/encode/bedRrbs.sql
- lines changed 23, context: html, text, full: html, text
Moving the as files to the lib/encode directory so they are all together at least.
- src/hg/lib/encode/broadPeak.as
- lines changed 5, context: html, text, full: html, text
First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
- src/hg/lib/encode/chiaPet.as
- lines changed 1, context: html, text, full: html, text
First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
- lines changed 12, context: html, text, full: html, text
Chia pet was never used, we used bed12 instead. shortFrags are download only
- src/hg/lib/encode/chiaPet.sql
- lines changed 19, context: html, text, full: html, text
Chia pet was never used, we used bed12 instead. shortFrags are download only
- src/hg/lib/encode/cshlShortTransfrag.as
- lines changed 30, context: html, text, full: html, text
First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
- src/hg/lib/encode/encodeExp.c
- lines changed 14, context: html, text, full: html, text
hgEncodeApi cleanup - retire encodeExpId request. Merge functionality into experiments request (it now filters on db= parameter)
- lines changed 23, context: html, text, full: html, text
hgEncodeApi and hgApi cleanup complete
- src/hg/lib/encode/gappedPeak.as
- lines changed 4, context: html, text, full: html, text
First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
- lines changed 1, context: html, text, full: html, text
Changing score to int to match bed standard
- src/hg/lib/encode/narrowPeak.as
- lines changed 6, context: html, text, full: html, text
First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
- src/hg/lib/encode/obsolete/shortFrags.as
- lines changed 31, context: html, text, full: html, text
Chia pet was never used, we used bed12 instead. shortFrags are download only
- src/hg/lib/encode/obsolete/shortFrags.sql
- lines changed 37, context: html, text, full: html, text
Chia pet was never used, we used bed12 instead. shortFrags are download only
- src/hg/lib/encode/shortFrags.as
- lines changed 31, context: html, text, full: html, text
Chia pet was never used, we used bed12 instead. shortFrags are download only
- src/hg/lib/encode/shortFrags.sql
- lines changed 37, context: html, text, full: html, text
Chia pet was never used, we used bed12 instead. shortFrags are download only
- src/hg/lib/encode/tagAlign.as
- lines changed 1, context: html, text, full: html, text
First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
- src/hg/lib/encode/wgEncodeGencodeExonSupport.as
- lines changed 3, context: html, text, full: html, text
Makeing the chromStart and chromEnd standard uint and standardizing the descriptions
- lines changed 1, context: html, text, full: html, text
First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
- src/hg/lib/encode/wgEncodeGencodeExonSupport.c
- src/hg/lib/encode/wgEncodeGencodeExonSupport.sql
- src/hg/lib/encode/wgEncodeGencodePolyAFeature.as
- lines changed 7, context: html, text, full: html, text
Makeing the chromStart and chromEnd standard uint and standardizing the descriptions
- lines changed 2, context: html, text, full: html, text
First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
- src/hg/lib/fullBed.as
- lines changed 1, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/lib/fullBed.sql
- lines changed 1, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/lib/gpFx.c
- lines changed 104, context: html, text, full: html, text
interim check-in for #6152. Adding variant structure and setup that allows maintaing multiple variants in one gp.
- lines changed 24, context: html, text, full: html, text
on-going work on annoGrator (#6152). Started using Sequence Ontology numbers from EBI, and added a generic variant structure as input to gpFx library
- src/hg/lib/jksql.c
- lines changed 3, context: html, text, full: html, text
advancing to the next stage in the mysql load correct warnings detection and abort
- src/hg/lib/makefile
- lines changed 1, context: html, text, full: html, text
interim check-in for #6152. Adding variant structure and setup that allows maintaing multiple variants in one gp.
- lines changed 2, context: html, text, full: html, text
hgEncodeApi and hgApi cleanup complete
- src/hg/lib/pubsArticle.sql
- lines changed 1, context: html, text, full: html, text
html changed according to gregs corrections, suppress copyright notice for non-elsevier papers, suppress document type for publishers that have only one type (main text) (comment from larrym), many many indentation corrections to better comply to jim kent source style (larrym comments)
- src/hg/lib/tests/annoGratorTester.c
- lines changed 1, context: html, text, full: html, text
on-going work on annoGrator (#6152). Started using Sequence Ontology numbers from EBI, and added a generic variant structure as input to gpFx library
- src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
- lines changed 9, context: html, text, full: html, text
on-going work on annoGrator (#6152). Started using Sequence Ontology numbers from EBI, and added a generic variant structure as input to gpFx library
- src/hg/lib/tests/expected/annoGrator/snpConsDbToTabOutShort.txt
- lines changed 38, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): include wiggle base positions,not just values, in tab-sep output because the wiggle values may be
available for only some of the primary row's bases.
- src/hg/lib/variant.c
- lines changed 56, context: html, text, full: html, text
interim check-in for #6152. Adding variant structure and setup that allows maintaing multiple variants in one gp.
- lines changed 4, context: html, text, full: html, text
on-going work on annoGrator (#6152). Started using Sequence Ontology numbers from EBI, and added a generic variant structure as input to gpFx library
- src/hg/makeDb/doc/danRer7.txt
- lines changed 8, context: html, text, full: html, text
change NCBI Incident to GRC Incident
- src/hg/makeDb/doc/dasNov3.txt
- lines changed 319, context: html, text, full: html, text
initial browser build through masking
- src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuHistone.release1.notes
- lines changed 4, context: html, text, full: html, text
Loaded fixed Peak files with correct p and q values. Redmine #111.
- src/hg/makeDb/doc/felCat5.txt
- lines changed 490, context: html, text, full: html, text
initial browser build through masking
- src/hg/makeDb/doc/hetGla2.txt
- lines changed 319, context: html, text, full: html, text
running masking on new genome sequences
- lines changed 46, context: html, text, full: html, text
initial browsers done through masking
- src/hg/makeDb/doc/hg19.txt
- lines changed 7, context: html, text, full: html, text
change NCBI Incident to GRC Incident
- src/hg/makeDb/doc/mm10.txt
- lines changed 478, context: html, text, full: html, text
initial 60way multiz calculations and running oreNil2 lastz done
- lines changed 183, context: html, text, full: html, text
running lastz on susScre dasNov3 and felCat5
- lines changed 191, context: html, text, full: html, text
done with lastz to hetGla2 turTru2 and nomLeu2
- src/hg/makeDb/doc/mm9.txt
- lines changed 7, context: html, text, full: html, text
change NCBI Incident to GRC Incident
- src/hg/makeDb/doc/nomLeu2.txt
- lines changed 370, context: html, text, full: html, text
download sequence from NCBI
- lines changed 108, context: html, text, full: html, text
running masking on new genome sequences
- lines changed 115, context: html, text, full: html, text
initial browsers done through masking
- src/hg/makeDb/doc/oreNil2.txt
- lines changed 199, context: html, text, full: html, text
starting new nile tilapia assembly
- lines changed 36, context: html, text, full: html, text
initial browser build complete
- lines changed 195, context: html, text, full: html, text
masked sequence is ready to go
- src/hg/makeDb/doc/strPur4.txt
- src/hg/makeDb/doc/susScr3.txt
- lines changed 66, context: html, text, full: html, text
initial browser build through masking
- src/hg/makeDb/doc/turTru2.txt
- lines changed 158, context: html, text, full: html, text
sequence assembled, browser built
- lines changed 211, context: html, text, full: html, text
running masking on new sequence
- lines changed 50, context: html, text, full: html, text
done through masking for initial browser
- src/hg/makeDb/genbank/etc/align.dbs
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 1, context: html, text, full: html, text
oops... had the wrong name for strPur4's 11.ooc
- src/hg/makeDb/hgLoadBed/hgLoadBed.c
- lines changed 153, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/hg/makeDb/schema/all.joiner
- lines changed 4, context: html, text, full: html, text
added grcIncidentDb and removed the now defuct ncbiIncidentDb table name from tables igonored for hg, mm, danRer
- src/hg/makeDb/trackDb/armadillo/dasNov3/description.html
- lines changed 132, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/armadillo/dasNov3/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/armadillo/dasNov3/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/armadillo/dasNov3/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 8, context: html, text, full: html, text
Fixed errors found by cvValidate upgrade.
- lines changed 1, context: html, text, full: html, text
Beginning derivedFrom to childOf migration in CV
- lines changed 1, context: html, text, full: html, text
Moved over approved changes from beta/cv.ra to public/cv.ra. In addition fixed accidently protocol renaming for MEF cell line in alpha/cv.ra. Redmine #7583.
- lines changed 44, context: html, text, full: html, text
Adding labels to Biochain tissues in CV
- lines changed 136, context: html, text, full: html, text
Adding BioChain parental cell types and moving derivedFrom to childOf
- lines changed 82, context: html, text, full: html, text
Fixing Code Review issues in CV
- lines changed 17, context: html, text, full: html, text
Adding parental line Lymphoblastoid cell line to CV
- lines changed 1, context: html, text, full: html, text
Resolving multiple childOf vars in CV for subclone of GM12878 stanza for Jim
- lines changed 1, context: html, text, full: html, text
Altering GM12878-XiMat childOf in CV
- lines changed 280, context: html, text, full: html, text
Moving H1-neurons and LHCN to tier 2
- lines changed 34, context: html, text, full: html, text
Adding newly promoted to tier 2 to description for H1 and LHCN
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 439, context: html, text, full: html, text
Pushing alpha CV to beta
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 459, context: html, text, full: html, text
Moved over approved changes from beta/cv.ra to public/cv.ra. In addition fixed accidently protocol renaming for MEF cell line in alpha/cv.ra. Redmine #7583.
- src/hg/makeDb/trackDb/dolphin/turTru2/description.html
- lines changed 132, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/dolphin/turTru2/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/dolphin/turTru2/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/gibbon/nomLeu2/description.html
- lines changed 132, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/gibbon/nomLeu2/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/gibbon/nomLeu2/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/gibbon/nomLeu2/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/grcIncidentDb.html
- lines changed 26, context: html, text, full: html, text
html for grcIncidentDb track
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 1, context: html, text, full: html, text
add xxxUncBsuProtGenc track
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 198, context: html, text, full: html, text
added accession numbers to CaltechRnaSeq
- lines changed 118, context: html, text, full: html, text
changed None to ilNA for insertLength
- lines changed 146, context: html, text, full: html, text
re-added accession numbers for Caltech RNA seq
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProtGenc.ra
- lines changed 5, context: html, text, full: html, text
creating basic trackDb and metaDb for xxxUncBsuProtGenc tracks
- lines changed 297, context: html, text, full: html, text
update with new submissions
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCaltechRnaSeq.ra
- lines changed 2491, context: html, text, full: html, text
Staging Caltech RNA-seq (Release 3) Fix release on beta (redmine #7425)
- lines changed 198, context: html, text, full: html, text
Morgan added geoSampleAccession IDs (redmine #7425)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromChip.ra
- lines changed 272, context: html, text, full: html, text
Matt updated expIds (redmine #7577)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromFaire.ra
- lines changed 180, context: html, text, full: html, text
Matt updated expIds (redmine #7577)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSunyAlbanyTiling.ra
- lines changed 9, context: html, text, full: html, text
Matt updated expIds (redmine #7577)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwHistone.ra
- lines changed 1790, context: html, text, full: html, text
Releasing UW Histone (Release 4) to the RR (redmine #6809)
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Staging Caltech RNA-seq (Release 3) Fix release on beta (redmine #7425)
- lines changed 2, context: html, text, full: html, text
Releasing UW Histone (Release 4) to the RR (redmine #6809)
- lines changed 3, context: html, text, full: html, text
add xxxUncBsuProtGenc track
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release3.html
- lines changed 189, context: html, text, full: html, text
added in new release 3 html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release3.ra
- lines changed 1, context: html, text, full: html, text
added in new release 3 html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
- lines changed 42, context: html, text, full: html, text
Updates from Steve to ChIA-PET description
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
- lines changed 22, context: html, text, full: html, text
Fixing short labels to be shorter
- lines changed 22, context: html, text, full: html, text
Fixing steves requests #1664
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.ra
- lines changed 57, context: html, text, full: html, text
creating basic trackDb and metaDb for xxxUncBsuProtGenc tracks
- lines changed 13, context: html, text, full: html, text
fix typos in view name, remove view for hg19 search only results
- lines changed 54, context: html, text, full: html, text
update with new submissions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release4.html
- lines changed 8, context: html, text, full: html, text
qa fixes for uw histone html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release4.ra
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
adding oreNil2 to the build
- lines changed 1, context: html, text, full: html, text
adding dasNov3 to the build
- lines changed 1, context: html, text, full: html, text
adding susScr3 to the build
- lines changed 1, context: html, text, full: html, text
adding turTru2 to the build
- lines changed 2, context: html, text, full: html, text
adding nomLeu2 and hetGla2 to the build
- src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
- src/hg/makeDb/trackDb/moleRat/hetGla2/description.html
- lines changed 132, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/moleRat/hetGla2/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/moleRat/hetGla2/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
- lines changed 3, context: html, text, full: html, text
remove merge conflict line
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
- lines changed 151, context: html, text, full: html, text
Loaded fixed Peak files with correct p and q values. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 2, context: html, text, full: html, text
added accession numbers for UwDnase
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuTfbs.ra
- lines changed 864, context: html, text, full: html, text
staging patch for LICR TFBS (mm9), redmine# 7418
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrTfbs.ra
- lines changed 5444, context: html, text, full: html, text
releasing LICR TFBS (release 2), redmine# 5394 and releasing patch for PSU TFBS, redmine# 7418
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuTfbs.ra
- lines changed 864, context: html, text, full: html, text
releasing LICR TFBS (release 2), redmine# 5394 and releasing patch for PSU TFBS, redmine# 7418
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
include xxxSydhHist.release2.ra
- lines changed 1, context: html, text, full: html, text
add beta,product to the previous release
- lines changed 2, context: html, text, full: html, text
staging patch for LICR TFBS (mm9), redmine# 7418
- lines changed 4, context: html, text, full: html, text
releasing LICR TFBS (release 2), redmine# 5394 and releasing patch for PSU TFBS, redmine# 7418
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.html
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra
- lines changed 1, context: html, text, full: html, text
remove .html from the html file in the top stanza
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.html
- lines changed 3, context: html, text, full: html, text
changed the release date, removed a hyphen, an added a comma for LICR TFBS (Release 2), redmine# 5394
- lines changed 17, context: html, text, full: html, text
removed the rel=nofollow from for LICR TFBS (release 2) as this was deemed not needed, redmine# 5394
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
- lines changed 27, context: html, text, full: html, text
Loaded fixed Peak files with correct p and q values. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra
- src/hg/makeDb/trackDb/oreNil/oreNil2/description.html
- lines changed 132, context: html, text, full: html, text
original files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/oreNil/oreNil2/gap.html
- lines changed 64, context: html, text, full: html, text
original files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/oreNil/oreNil2/gold.html
- lines changed 23, context: html, text, full: html, text
original files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra
- lines changed 8, context: html, text, full: html, text
original files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/pig/susScr3/description.html
- lines changed 132, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/pig/susScr3/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/pig/susScr3/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 1, context: html, text, full: html, text
commiting files again, hopefully have not messed up my git
- src/hg/makeDb/trackDb/urchin/strPur4/description.html
- src/hg/makeDb/trackDb/urchin/strPur4/gap.html
- src/hg/makeDb/trackDb/urchin/strPur4/gold.html
- src/hg/makeDb/trackDb/urchin/strPur4/trackDb.ra
- src/hg/makeDb/trackDb/worm/ce2/description.html
- lines changed 1, context: html, text, full: html, text
Updated link to WormBase based on information from Todd Harris at WormBase
- src/hg/makefile
- lines changed 2, context: html, text, full: html, text
add ENCODE api CGI, that provides ajax calls for ENCODE Data Matrix application
- src/hg/mouseStuff/netStats/netStats.c
- lines changed 4, context: html, text, full: html, text
Changed name of local function to not conflict with global function. These cases were fallout from Galt's check-in, I believe. I am fixing these as per my duties as buildMeister
- src/hg/patCount/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/hg/scanRa/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/hg/splitFa/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
- lines changed 96, context: html, text, full: html, text
handle conversion of GFF3 files with UTR/CDS annotation but no exon records
- src/hg/utils/gff3ToGenePred/tests/expected/geneMRnaHonorTest.gp
- lines changed 1, context: html, text, full: html, text
handle conversion of GFF3 files with UTR/CDS annotation but no exon records
- src/hg/utils/gff3ToGenePred/tests/expected/geneMRnaTest.gp
- lines changed 1, context: html, text, full: html, text
handle conversion of GFF3 files with UTR/CDS annotation but no exon records
- src/hg/utils/gff3ToGenePred/tests/expected/noExonsTest.gp
- lines changed 19, context: html, text, full: html, text
handle conversion of GFF3 files with UTR/CDS annotation but no exon records
- src/hg/utils/gff3ToGenePred/tests/expected/noGeneMRnaTest.gp
- lines changed 2, context: html, text, full: html, text
handle conversion of GFF3 files with UTR/CDS annotation but no exon records
- src/hg/utils/gff3ToGenePred/tests/input/noExons.gff3
- lines changed 818, context: html, text, full: html, text
handle conversion of GFF3 files with UTR/CDS annotation but no exon records
- src/hg/utils/gff3ToGenePred/tests/makefile
- lines changed 5, context: html, text, full: html, text
handle conversion of GFF3 files with UTR/CDS annotation but no exon records
- src/hg/utils/phyloTrees/62way.nh
- lines changed 7, context: html, text, full: html, text
fixing this tree based on Bob's input
- lines changed 7, context: html, text, full: html, text
updating to nomLeu2, hetGla2, susScr3, turTru2, felCat4, dasNov3, oreNil2
- src/inc/asParse.h
- lines changed 16, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/inc/basicBed.h
- lines changed 11, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/inc/linefile.h
- lines changed 30, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/index/indexfa/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/index/indexgl/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/index/ixali/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/index/ixword1/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/index/ixword3/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/index/makepgo/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/index/stToXao/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/lib/annoFormatTab.c
- lines changed 68, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): include wiggle base positions,not just values, in tab-sep output because the wiggle values may be
available for only some of the primary row's bases.
- src/lib/annoGrator.c
- lines changed 2, context: html, text, full: html, text
Bugfix for #6152: when checking range overlap, don't forget to checkthat chroms are the same too since annoGrator's queue can end with the
first item from the next chrom.
- src/lib/asParse.c
- lines changed 191, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/lib/basicBed.c
- lines changed 322, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/lib/bbiWrite.c
- lines changed 6, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/lib/linefile.c
- lines changed 267, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/lib/tests/makefile
- lines changed 15, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/primeMate/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/protDust/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/reformat/fatont4/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/reformat/gb2cdi/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/reformat/gbtofa/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/reformat/geniegff/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/reformat/gffgenes/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/reformat/moresyn/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/scanIntrons/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/tracks/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/utils/addCols/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/utils/asCompare/asCompare.c
- lines changed 65, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/utils/asCompare/makefile
- lines changed 20, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/utils/aveCols/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/utils/bedToBigBed/bedToBigBed.c
- lines changed 122, context: html, text, full: html, text
This is a squashed merge to make git-reports code-review simpler.
The main thing is that there is a new shared validator routine in lib/basicBed.c
which uses asParse.c to handle bedPlus.
This validator is shared among validateFiles, bedToBigBed, hgLoadBed, and customTracks.
Some effort has been made to standardize commandline options,
and vf has been simplified a little by removing some debugging options.
vf has also recently gaind the ability to validate native bigBed format,
via some new code in linefile.c for attaching to a bigBed.
ct: use of the new validator is controlled by an hg.conf flag that
can be turned on and if needed turned off again. It will be off
by default for now. As soon as we are happy with the code
and it has been established, we can remove the switch.
Code has been added to compare .as files,
and it is here used to compare against the library standard BED.
As an experiment I am leaving in the list of squashed commits messages below:
Squashed commit of the following:
commit a55eb050055911c699120432cc98e33cefa5fffc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 17:00:30 2012 -0700
fixing freeMem bug; making better option-combination checking, fixing as, adding test bed6
commit ac4b98f41e89875bc100cd2f1c1fc3825cafa57d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Apr 13 12:56:32 2012 -0700
unless we add back in everywhere the -zerosOk option, we must tolerate them for SNP type objects
commit efa2c269a6df4ea0630084670d152b4d518e232b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 16:16:46 2012 -0700
adding bed15 example input
commit f2b5af00e2786283e785ef501caa036e5a945dc7
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:09:18 2012 -0700
increasing maximum row length buffer automatically in lineFile on bigbed
commit 1bb07ce21fcd4ce1d55752b0b61997ffb71a159e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 11:03:59 2012 -0700
increasing maximum row length buffer automatically
commit 59e831df690c5b8ac68afc9648443b3cb5dfd51b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Apr 12 10:45:22 2012 -0700
increasing maximum row length buffer
commit 711db7c2edf0a6f7b710fde1929af1ba388cb81d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 23:45:18 2012 -0700
adding lineFileOnBigBed, using it to add bigBed validation to validateFiles.
commit 1b5e5e1eaba802c25c94a8a3dd000898d2fb3150
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 17:01:49 2012 -0700
for consistency with basicBed.c
commit ca8e7f93af179803f4a6fe2d073703f379e271a3
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 16:55:26 2012 -0700
standardizing - have to call the field "reserved" so that .sql will contain the right name and existing trackhandlers will work
commit fea0cb3bb7163353496c3d092d3716f1b5c30e53
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 11 12:12:25 2012 -0700
renaming option -tabs to -tab to be consistent with hgLoadBed
commit 6452f634c4cc7730b521869cdfb11f4253c59ff5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:44:11 2012 -0700
trap aborts from weird errs reading as files
commit 9800e8416b5959d7a80f3785e116987569e7273c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:14:05 2012 -0700
oops
commit f9f1b7f9d9e136864df4b908cd32773e1a04a260
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 18:08:13 2012 -0700
adding asCompare utility for comparing a given .as against many others
commit 605f9a9da14b3a168821519eba737b7f4cd48163
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 15:17:11 2012 -0700
add parameter to return the number of columns that did match the give .as, even if the entire match might fail
commit 86fb68307dfbefd2960c9173fbbae1c4d4c49b11
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 12:00:24 2012 -0700
adding a handy standard bed12 .as file for testing
commit 79bd2364e383e133c886d034a9176c6e636181cc
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 11:27:09 2012 -0700
added support for linked-Size in .as validation so that list sizes get validated
commit 67ee8435b668f779fce28744519e5e76d6ae3433
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 10 09:53:19 2012 -0700
oops signed flag was backwards
commit ebae2bef410150aefd39b7b01918fbc8c18e6785
Merge: ab0cee9 8f806f5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:28:10 2012 -0700
Merge commit 'origin/master' into validateFiles
commit ab0cee922869996045074c6076c38abd8487d7c2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 16:15:53 2012 -0700
fixing rgb
commit 4187a167aeeb69eb20ad9df8021db9c8f71d9193
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:42:27 2012 -0700
updated testing files
commit 0ee0c51132cb09a4e9909caa9718bdf7aa5af9ff
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:33:42 2012 -0700
fix err msg bug where colors field had already been chopped up by the parser
commit edeed9458c345d1d8629d1e1b5230eb6b9e424a8
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 14:16:27 2012 -0700
adding -tabs option but making whitespace the default. this is to make it like b2bb and hglb
commit 239ca9b99d04b7ff6817867160b34efe8af1d25a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:35:06 2012 -0700
more printf fixes %d ==> %u
commit 57745b3096c096d73b02a651cba0060210acad07
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 12:19:46 2012 -0700
fixing some %d to %u for correct sign of bed struct members in printf
commit 7c3f3f24402f01f2f152f6b839b9efb01fa9c5c1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:33:30 2012 -0700
oops need to use FromDatabase with chromDb option
commit 237ab4c1b707ba19ba12079483365269db3b6119
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Apr 9 09:26:43 2012 -0700
little fix removing unused option maxErrors
commit 689c10edba73f49658f315a14201468864e5d83c
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Sun Apr 8 12:07:04 2012 -0700
reducing redundancy by making allInts both polymorphic and fast; added checking of .as fields against BED standard for the first bedN columns
commit c6bd5e6eec93c4ca6e947e7028907110e4e73d0e
Merge: 4d09bfd b7b8f22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Apr 4 12:58:34 2012 -0700
Merge commit 'origin/master' into validateFiles
commit 4d09bfdd35087b6637fa638297be9c07b45cb450
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:31:32 2012 -0700
because tabs may be used, cannot confirm here that the strings are non-empty, because they might be, so removing the check
commit cfaa756790ee029e480a045f05a51733ebef4e4b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:25:03 2012 -0700
adding back the check for chrHash (chromDb or chromInfo) that was lost when I reverted the tabs option deletion
commit 5531303fe2ee39d28cec7c9f4baa472ce0ab5eba
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:20:27 2012 -0700
Revert "cleaned up unneeded options, using chopByWhite instead of chopByTab."
This reverts commit 458a52f976edade78177908bc9f5886c81e7b6ab.
commit 0ea039f35541360ca1d64d754af3f9dec6621a38
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Apr 3 14:15:45 2012 -0700
resolved reversion of fa3b343f1ff1eb7a50df9029e71141484f260a22
commit 44e7cbc4dbf3b5a955f7fa1eea6a65a7d8570528
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:34:47 2012 -0700
removed unneeded errs variable
commit 404c095271351b38233124e74cd35cbc57b8aad4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:10:27 2012 -0700
removed line count variable
commit 5561bd6a7b85e6115f8162eb2e597de0f7c2c284
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 16:06:03 2012 -0700
removed unneeded flags printFailLines printOkLines, and quick
commit 5a6eae96483d91baa7690df436d4becc13cdbf2f
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:10:13 2012 -0700
jk prefers brackets to curly-braces
commit 7e431a76a215c1402c5a6a37816f6fc7ca234363
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Mar 29 15:01:45 2012 -0700
adding version # for b2bb, by crickets request
commit fa3b343f1ff1eb7a50df9029e71141484f260a22
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:43:33 2012 -0700
removed -tabs option, using chopByWhite instead of chopByTab because of bed definition according to JK
commit 458a52f976edade78177908bc9f5886c81e7b6ab
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:40:10 2012 -0700
cleaned up unneeded options, using chopByWhite instead of chopByTab.
commit 7e179aab9da9961221bf864fdd136ed8bbc0392b
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 16:13:30 2012 -0700
removing zeroSizeOk option
commit 8c8ad8ca09239b7a7a8cc0de693b8a7c7d49a669
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 15:51:45 2012 -0700
improving the wording of help
commit 1bf63d9d7e7fa89e060eab26a9751acd3c8ad8e4
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:37:37 2012 -0700
changing edge-case definition slightly for chromEnd
commit 7e5c151234e12cd8b55d10e79042d7f92b3fcb5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 12:04:29 2012 -0700
incrementing version
commit c0e129d917eaac888e6a9c521c4407bf9380b4b0
Merge: f6ce988 68a21eb
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Mar 28 11:16:45 2012 -0700
Merge commit 'origin/master' into validateFiles
commit f6ce988fb6f76bb74439c77c4094483f26465c90
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 15:39:54 2012 -0800
oops
commit 3dfdebd293e93073354f9af486a7d9407f0b9471
Merge: cf104e3 75c9145
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:59:58 2012 -0800
Merge commit 'origin/master' into validateFiles
commit cf104e362325a5832911022865bb69241e1e472d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:55:23 2012 -0800
adding hg.conf switch to activate new validator use
commit ef5806814a6e9730682ea56a0a0e45ab962a9ee1
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 8 14:26:43 2012 -0800
various cleanup and consistency
commit 3e4e92b25cf414129ba0339a91023380c2f8f974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Feb 3 17:21:51 2012 -0800
adding chromDb, and chromInfo options to hgLoadBed
commit 05ed14c1e92684861789163e3c936bf07778acb2
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 21:06:55 2012 -0800
added optional validation support for bed and bedPlus to hgLoadBed
commit 7445f19ac4009eed47b989999de35f92b550fac5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Feb 1 20:09:54 2012 -0800
tested bedPlus, and extended checking for more types/cases, e.g. string~ and unsigned numbers
commit 31b44ec97ecd57101b3c65096288347592276d5d
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 31 11:11:07 2012 -0800
adding support for context during array-list parsing
commit 5ffcc5974b59f00551940f0dc20b56f1e7990f12
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Mon Jan 30 11:15:12 2012 -0800
re-working things, adding better checking
commit 46e10b9ff5d32793656dfd1d136687f2a0733b4e
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 17:28:41 2012 -0800
validateFiles now supports bed, bedPlus using the shared validator lib function
commit d2adfda8e080b562c93084f956ddcdcf47f06974
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Fri Jan 20 02:33:09 2012 -0800
cleanup, handling ct differently than the others which care only for validation but not the actual bed results
commit 1fe9aa5028374750a491a0a3f836f4657f9b9a43
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:54:12 2012 -0800
added support for bedPlus via .as object
commit 7b32efb4152f57038ae56d3dca15fd700398ea5a
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Thu Jan 19 16:13:40 2012 -0800
moved validation code from customFactory.c to basicBed.c, added validation support to b2bb
commit 64b293690baeb50ce375f34e01493dbc9a50cbf5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 17 14:06:35 2012 -0800
ok, have bed 12 linked-features validation working
commit f0a6d2c2a749fffedadc8189ff7ba86583003128
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:37:10 2012 -0800
adding README describing how some bed tests are made
commit 46400cceb3a602423ae2a5656bc442d9969e63df
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Wed Jan 11 11:26:13 2012 -0800
fixed bigwig tests; added bed12ok test
commit 305e5c0e07210d278aa257d7c859bdd47abc77c5
Author: Galt Barber <galt@soe.ucsc.edu>
Date: Tue Jan 10 17:05:13 2012 -0800
added support for bed files (not including bedPlus); also began working on re-organizing the make test cases
- src/utils/catUncomment/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/utils/ccCp/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/utils/chopFaLines/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/utils/countChars/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/utils/faNoise/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/utils/faOneRecord/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/utils/faSplit/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/utils/findMotif/findMotif.c
- lines changed 4, context: html, text, full: html, text
Changed name of global var to avoid conflict with Galt's lib changes.
- src/utils/fixCr/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/htmlPics/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/jkUniq/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/newProg/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/nibFrag/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/nibSize/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/qa/checkGenomeMysql
- lines changed 33, context: html, text, full: html, text
No longer checking to see that RR table dumps and genome-mysql are in sync (they usually are not). Changed to rely only on MySQL errors being reported, and to check both genome-mysql servers (Redmine #3457).
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/qa/weeklybld/doNewBranch.csh
- lines changed 2, context: html, text, full: html, text
Galt pointed out a better way of bracketing the git command used to determine the cycle's check-ins.
- src/utils/qa/weeklybld/summaryEmail.sh
- lines changed 2, context: html, text, full: html, text
Galt pointed out a better way of bracketing the git command used to determine the cycle's check-ins.
- src/utils/rmFaDups/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/scaffoldFaToAgp/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/scrambleFa/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/subChar/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/toLower/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/toUpper/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/undupFa/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/upper/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/utils/wordLine/makefile
- lines changed 1, context: html, text, full: html, text
Another batch of makefile changes to add -lm
- src/weblet/counter/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/weblet/hitreport/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- src/xenoAli/bwana/makefile
- lines changed 1, context: html, text, full: html, text
Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code.
- lines changed: 1229097
- files changed: 403