All File Changes
v248_base to v249_preview (2011-03-08 to 2011-03-15) v249
- src/hg/autoXml/makefile
- lines changed 2, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/bedOverlap/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/chimpStuff/chimpHiQualDiffs/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/chimpStuff/chimpSuperQuals/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf
- lines changed 2, context: html, text, full: html, text
Added validation setting that verifies that at least 99.9% of the bams have at most 3 mismatches.
- lines changed 1, context: html, text, full: html, text
Added matchFirst and nmatch options that lab requested.
- src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf
- lines changed 2, context: html, text, full: html, text
Added validation setting that verifies that at least 99.9% of the bams have at most 3 mismatches.
- lines changed 1, context: html, text, full: html, text
Added matchFirst and nmatch options that lab requested.
- src/hg/encode/DAFs/2.0/uMassDekker5c.daf
- src/hg/encode/DAFs/2.0/uw5c.daf
- src/hg/encode/autoSql/bedRrbs.as
- lines changed 2, context: html, text, full: html, text
oops... score field has to be named score
- src/hg/encode/autoSql/bedRrbs.sql
- lines changed 1, context: html, text, full: html, text
oops... score field has to be named score
- src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
- lines changed 1, context: html, text, full: html, text
Added bedRrbs as a file type to handle
- src/hg/encode/encodeMkChangeNotes/makefile
- lines changed 3, context: html, text, full: html, text
install and alpha put it in /cluster/bin/scripts, otherwise $HOME/bin/scripts
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- src/hg/encode/encodeValidate/makefile
- lines changed 3, context: html, text, full: html, text
copy the alpha cv.ra file into the downloads directory if we're doing a make install. This allows the labs to grab the same cv.ra we're using in the pipeline.
- src/hg/encode/metaCheck/README.txt
- lines changed 26, context: html, text, full: html, text
a little more detail about what metaCheck does
- src/hg/encode/metaCheck/metaCheck.c
- lines changed 6, context: html, text, full: html, text
a little more detail about what metaCheck does
- src/hg/geneBounds/lib/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/geneOverlap/makefile
- lines changed 2, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/hgApi/hgApi.c
- lines changed 24, context: html, text, full: html, text
Moved a few functions common to track search and file search into library code. Redesigned a few things to standardize on slPair lists of vals and labels.
- lines changed 6, context: html, text, full: html, text
Changed mdb API required this change.
- src/hg/hgFileSearch/hgFileSearch.c
- lines changed 310, context: html, text, full: html, text
Moved a few functions common to track search and file search into library code. Redesigned a few things to standardize on slPair lists of vals and labels.
- lines changed 1, context: html, text, full: html, text
Fixing Ubuntu gcc warnings by using puts instead of printf-without-format.
- src/hg/hgFileUi/hgFileUi.c
- lines changed 8, context: html, text, full: html, text
Added NAFV link to track description at bottom of page.
- src/hg/hgGene/hgGene.c
- lines changed 2, context: html, text, full: html, text
Adding hgBotDelay call to hgGene to avoid bot damage like we got yesterday.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 2, context: html, text, full: html, text
SuperTracks offer links to hgFileUi CGI if the tdb says downloadsOnly
- lines changed 10, context: html, text, full: html, text
Added support for showing downloadsOnly tracks in hgTracks (but only if they are part of a superTrack with other visible tracks). Also standardized links for downloadsOnly tacks between hgTracks and hgTrackUi
- lines changed 60, context: html, text, full: html, text
Added filters for new OMIM tracks.
- lines changed 6, context: html, text, full: html, text
Feature/Bug #3148 (DGV description page refs): fixing bug found by b0b:the filter on PubMed references was set to "include" by default, but all
checkboxes were empty by default. Fix: if the checkbox group variable is
not defined in the cart, then set all checkboxes.
- src/hg/hgTracks/bamTrack.c
- lines changed 36, context: html, text, full: html, text
put out one mapBox per row if there are too many individual items #1279
- src/hg/hgTracks/bedTrack.c
- lines changed 28, context: html, text, full: html, text
Track #34 (dbVar for human): Hooked up next/prev exon methodfor simple bed tracks, which simply hops to right edge/left edge
of items hanging off the end of the window.
- src/hg/hgTracks/config.c
- lines changed 43, context: html, text, full: html, text
Added support for showing downloadsOnly tracks in hgTracks (but only if they are part of a superTrack with other visible tracks). Also standardized links for downloadsOnly tacks between hgTracks and hgTrackUi
- src/hg/hgTracks/searchTracks.c
- lines changed 353, context: html, text, full: html, text
Moved a few functions common to track search and file search into library code. Redesigned a few things to standardize on slPair lists of vals and labels.
- lines changed 1, context: html, text, full: html, text
Fixing Ubuntu gcc warnings by using puts instead of printf-without-format.
- src/hg/hgTracks/simpleTracks.c
- lines changed 264, context: html, text, full: html, text
Updated functions for new OMIM tracks.
- src/hg/hgTracks/variation.c
- lines changed 14, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): oops, overwriting snp125->name whenchimp allele is added (in dbb7cbfd) caused the name+allele string to
be passed to hgc as the item name, which causes an errAbort because
the item can't be found. So now we need a mapItemName that strips
off the allele string if any is added.
- src/hg/hgc/bamClick.c
- lines changed 3, context: html, text, full: html, text
put out one mapBox per row if there are too many individual items #1279
- src/hg/hgc/hgc.c
- lines changed 29, context: html, text, full: html, text
Updated funtions for new OMIM tracks.
- src/hg/hgc/hgdpClick.c
- lines changed 7, context: html, text, full: html, text
Bug #3208 (hg19 HGDP Allele Freq hgc position links are broken):doh, using a *StaticLoad and then immediately doing a sqlFreeResult
is a bad idea. No need to scrounge for memory w/StaticLoad in hgc.
- src/hg/hgcentralTidy/hgcentralTidy.c
- lines changed 412, context: html, text, full: html, text
adding new hgcentralTidy; apologies to code reviewers that there are still comments in the code. this has been a work in progress but has reached the point of being useful for production.
- src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
- src/hg/htdocs/images/Meleagris_gallopavo.jpg
- src/hg/htdocs/makefile
- lines changed 1, context: html, text, full: html, text
don't update the styles with make beta in htdocs
- src/hg/htdocs/style/HGStyle.css
- lines changed 2, context: html, text, full: html, text
The filterBy multi-selects that use ui-dropdownchecklist.js must be initially hidden.
- src/hg/htdocs/style/cpAndLinkToResourceFiles.pl
- lines changed 94, context: html, text, full: html, text
coallesce cpAndLinkToResourceFiles.pl
- src/hg/htdocs/style/makefile
- lines changed 1, context: html, text, full: html, text
add jquery.ui.autocomplete.css
- lines changed 1, context: html, text, full: html, text
change path to cpAndLinkToResourceFiles (which has been moved)
- src/hg/inc/cart.h
- lines changed 6, context: html, text, full: html, text
While working on something else, I realized that when cartRemove iscalled on a list variable, it should remove the list's multShadow
variable in addition to all values, because the list variable is no
longer defined in the cart. If the multShadow is left around, it will
look like the variable is in the cart, set to empty.
- src/hg/inc/hdb.h
- lines changed 4, context: html, text, full: html, text
For download file lookup, beta should look on hgdownloads-test but in beta/ subdirectory.
- src/hg/inc/mdb.h
- lines changed 5, context: html, text, full: html, text
Subtle change to the mdbValLabelSearch() API to put the required val in the pair->name and the optional label in the pair->val. This helps standardize other code that deals with val/label pairs, and enables using slPairFind().
- lines changed 11, context: html, text, full: html, text
Added const to a couple of APIs and changed some stuff to aid fleUi filterFiles functionality
- src/hg/inc/searchTracks.h
- lines changed 27, context: html, text, full: html, text
Moved a few functions common to track search and file search into library code. Redesigned a few things to standardize on slPair lists of vals and labels.
- src/hg/js/hgTracks.js
- lines changed 1, context: html, text, full: html, text
redmine 2916. IE is finiky about extra commas.
- src/hg/js/makefile
- lines changed 5, context: html, text, full: html, text
make the DOCUMENTROOT logic match that in kent/src/hg/htodcs/style/makefile to handle user-specific htdocs sandboxes
- lines changed 1, context: html, text, full: html, text
cpJsFiles => cpAndLinkToResourceFiles.pl
- src/hg/js/ui.dropdownchecklist.js
- lines changed 5, context: html, text, full: html, text
Added filterBy boxes to hgFileUi to allow slimiting the number of files seen on the page
- src/hg/js/utils.js
- lines changed 169, context: html, text, full: html, text
Added filterBy boxes to hgFileUi to allow slimiting the number of files seen on the page
- lines changed 1, context: html, text, full: html, text
Empty multi-select resulted in browser errors.
- src/hg/lib/cart.c
- lines changed 49, context: html, text, full: html, text
While working on something else, I realized that when cartRemove iscalled on a list variable, it should remove the list's multShadow
variable in addition to all values, because the list variable is no
longer defined in the cart. If the multShadow is left around, it will
look like the variable is in the cart, set to empty.
- src/hg/lib/clusterInputTrackTable2.as
- lines changed 8, context: html, text, full: html, text
More work on new TFBS clustering stuff.
- src/hg/lib/clusterInputTrackTable2.sql
- lines changed 17, context: html, text, full: html, text
More work on new TFBS clustering stuff.
- src/hg/lib/fileUi.c
- lines changed 108, context: html, text, full: html, text
For download file lookup, beta should look on hgdownloads-test but in beta/ subdirectory.
- lines changed 152, context: html, text, full: html, text
Added filterBy boxes to hgFileUi to allow slimiting the number of files seen on the page
- lines changed 1, context: html, text, full: html, text
filterFiles boxes should have bold titles. We want people to notice.
- lines changed 1, context: html, text, full: html, text
Preview host should not rsync but should use ls into it's filesystem. What about hgwbeta?
- src/hg/lib/hdb.c
- lines changed 7, context: html, text, full: html, text
For download file lookup, beta should look on hgdownloads-test but in beta/ subdirectory.
- lines changed 1, context: html, text, full: html, text
Kate suggested that 'genome-test' would be retargeted to 'genome-preview' but this hasn't happened yet.
- src/hg/lib/hui.c
- lines changed 2, context: html, text, full: html, text
Removing from metadata mdb vars defined as hidden by cvv.ra
- lines changed 3, context: html, text, full: html, text
Should be retiring ui.code.js as jquery-ui.js is a superset.
- src/hg/lib/knownCanonical.as
- lines changed 1, context: html, text, full: html, text
Updating protein column description in knownCanonical to reflect UCSC IDs instead of SwissProt.
- src/hg/lib/mdb.c
- lines changed 73, context: html, text, full: html, text
Subtle change to the mdbValLabelSearch() API to put the required val in the pair->name and the optional label in the pair->val. This helps standardize other code that deals with val/label pairs, and enables using slPairFind().
- lines changed 2, context: html, text, full: html, text
Fix a couple of small bugs I just introduced to track/file searches
- lines changed 65, context: html, text, full: html, text
Added const to a couple of APIs and changed some stuff to aid fleUi filterFiles functionality
- src/hg/lib/searchTracks.c
- lines changed 241, context: html, text, full: html, text
Moved a few functions common to track search and file search into library code. Redesigned a few things to standardize on slPair lists of vals and labels.
- lines changed 3, context: html, text, full: html, text
Fix a couple of small bugs I just introduced to track/file searches
- lines changed 10, context: html, text, full: html, text
Changed mdb API required this change.
- src/hg/lib/trackDbCustom.c
- lines changed 1, context: html, text, full: html, text
Track #34 (dbVar for human): new track type gvf needs to be made packable in trackDbCustom.c. I forget this every time I make a new track type.
- src/hg/lib/web.c
- lines changed 7, context: html, text, full: html, text
use CGI version based softlinks for js and css files in production sites (see redmine 3170
- src/hg/logCrawl/hgAccessCrawl/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisChiaPet.release1.notes
- lines changed 0, context: html, text, full: html, text
Release notes for GisChiaPet
- lines changed 176, context: html, text, full: html, text
Added better release notes for Chia Pet
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release2.notes
- lines changed 342, context: html, text, full: html, text
Updated file type from .bed9 to .bedRrbs
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyAlbanyGeneSt.release1.notes
- lines changed 4, context: html, text, full: html, text
removed extra / in 4 places
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunySwitchgear.release1.notes
- lines changed 48, context: html, text, full: html, text
New notes files for 2 files
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release1.notes
- lines changed 2, context: html, text, full: html, text
Removed 2 fastq files that were accidently left in notes file.
- lines changed 2, context: html, text, full: html, text
Updated the total file counts with accurate number of files available in download files.
- src/hg/makeDb/doc/hg19.txt
- lines changed 51, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): regenerated snp132 with updatedsnpNcbiToUcsc's -par option. Tweaked singly-mapped PAR SNPs' weights
to 1 (dbSNP agrees they should be 1 not 3 and plans to fix).
Regenerated subset tracks snp132{Common,Patient,NonUnique}.
- lines changed 99, context: html, text, full: html, text
Documented build process for new OMIM tracks.
- lines changed 119, context: html, text, full: html, text
Work on wgEncodeReg track.
- lines changed 79, context: html, text, full: html, text
Further work on wgEncodeReg.
- src/hg/makeDb/doc/melGal1.txt
- src/hg/makeDb/doc/panTro3.txt
- lines changed 83, context: html, text, full: html, text
only monDom5 and mm9 chain net left to go
- src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
- lines changed 63, context: html, text, full: html, text
Some last bits of mouse UCSC genes redo I hope.
- src/hg/makeDb/genbank/etc/align-genbank
- src/hg/makeDb/genbank/etc/align.dbs
- lines changed 2, context: html, text, full: html, text
removed databases that are not needed
- src/hg/makeDb/genbank/etc/build.crontab
- src/hg/makeDb/genbank/etc/genbank.conf
- src/hg/makeDb/genbank/etc/hgwdev.crontab
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 2, context: html, text, full: html, text
removed databases that are not needed
- src/hg/makeDb/genbank/src/align/gbAlignCommon.h
- lines changed 5, context: html, text, full: html, text
avoid need to recheck indices when installing alignments if there is nothing to migrate or align
- src/hg/makeDb/genbank/src/align/gbAlignGet.c
- lines changed 14, context: html, text, full: html, text
avoid need to recheck indices when installing alignments if there is nothing to migrate or align
- src/hg/makeDb/genbank/src/align/gbAlignRSync
- lines changed 48, context: html, text, full: html, text
allow multiple databases to be run in parallel
- src/hg/makeDb/genbank/src/align/gbAlignSetup
- lines changed 1, context: html, text, full: html, text
avoid need to recheck indices when installing alignments if there is nothing to migrate or align
- src/hg/makeDb/genbank/src/align/gbAlignStep
- lines changed 155, context: html, text, full: html, text
allow multiple databases to be run in parallel
- src/hg/makeDb/genbank/src/align/makefile
- lines changed 1, context: html, text, full: html, text
allow multiple databases to be run in parallel
- src/hg/makeDb/genbank/src/lib/gbCommon.pm
- lines changed 13, context: html, text, full: html, text
allow multiple databases to be run in parallel
- src/hg/makeDb/hgTrackDb/hgTrackDb.c
- lines changed 28, context: html, text, full: html, text
Extended hgTrackDb's new #insert syntax: optionally it may be precededby a conditional on the database, e.g.
<!-- #if (db==hg19) #insert file="human/hg19/specialNote.html" -->
- src/hg/makeDb/mdbUpdate/mdbPrint.c
- lines changed 19, context: html, text, full: html, text
Slight change to allow -composite -vars and -var to all work simultaneously to create a single selection.
- src/hg/makeDb/schema/all.joiner
- lines changed 3, context: html, text, full: html, text
added ncbiIncidentDb to tablesIgnored for hg19,mm9,danRer7
- src/hg/makeDb/trackDb/README
- lines changed 3, context: html, text, full: html, text
Extended hgTrackDb's new #insert syntax: optionally it may be precededby a conditional on the database, e.g.
<!-- #if (db==hg19) #insert file="human/hg19/specialNote.html" -->
- src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra
- lines changed 5, context: html, text, full: html, text
adding chain net overrides for all panTro3 related chain net combinations
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 7, context: html, text, full: html, text
Accepted several provisional stanzas
- lines changed 5, context: html, text, full: html, text
More 5C data agreement work
- lines changed 20, context: html, text, full: html, text
Commented out submitPath and docId for now
- lines changed 29, context: html, text, full: html, text
Removed the , in the treatment description, replaced with a with
- lines changed 6, context: html, text, full: html, text
Accepted a couple provisional stanzas
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 18, context: html, text, full: html, text
pushing cv.ra with multiSelect instead of select to public since the v248 CGIs have been released and can support multiSelect, Redmine Issue 3085
- src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
- lines changed 5, context: html, text, full: html, text
adding chain net overrides for all panTro3 related chain net combinations
- src/hg/makeDb/trackDb/horse/trackDb.chainNet.ra
- lines changed 6, context: html, text, full: html, text
adding chain net overrides for all panTro3 related chain net combinations
- src/hg/makeDb/trackDb/human/affyExonArray.html
- lines changed 50, context: html, text, full: html, text
Updated the page for the Affy Exon array track, to reflect its new content
- lines changed 6, context: html, text, full: html, text
Added a short paragraph to the affy exon array track details page, describing what the identifiers represent. Added separate views for the probe and probeset subtracks, so that their iews can be set independently.
- src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
- lines changed 1, context: html, text, full: html, text
Fixed link to Reymond 'Nineteen...' article
- src/hg/makeDb/trackDb/human/hg18/description.html
- src/hg/makeDb/trackDb/human/hg18/encodeNhgriDukeDnaseHs.html
- lines changed 1, context: html, text, full: html, text
Fixed link for McArthur article
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- src/hg/makeDb/trackDb/human/hg19/description.html
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra
- lines changed 36, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 4537, context: html, text, full: html, text
Added the new elements data and some of the replacement data
- lines changed 578, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 2, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
- lines changed 2, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
- lines changed 298, context: html, text, full: html, text
Changed to have the one with a treatment show as a cell type, for Tier 1 and Tier 2 to filter to the top
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl27.ra
- lines changed 147, context: html, text, full: html, text
Cleaned up the meta data and the downloads display
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra
- lines changed 1466, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- lines changed 2, context: html, text, full: html, text
Corrected file names, .bed.gz > .bed9.gz
- lines changed 198, context: html, text, full: html, text
Changed file extensions from .bed9.gz to .bedRrbs.gz
- lines changed 198, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
- lines changed 230, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 24, context: html, text, full: html, text
Removed wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep1 from metaDb, on recommendation of Flo.
- lines changed 24, context: html, text, full: html, text
Removed reference to file wgEncodeHaibTfbsT47dCtcfV0416102Dmso2RawRep2, as per Flo.
- lines changed 1992, context: html, text, full: html, text
Added 8 submissions that included missing data and resubmitted files with updated meta-data.
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
- lines changed 275, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
- lines changed 119, context: html, text, full: html, text
resubmitted data so the metaData Changed
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwChIPSeq.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 2, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- lines changed 178, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 144, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleChIPseq.ra
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
- lines changed 66, context: html, text, full: html, text
Changed the polyA+ to polyA- for K562
- lines changed 2, context: html, text, full: html, text
Changed two typos in the fileNames
- lines changed 6, context: html, text, full: html, text
Added experimental variables to all composites
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwAffyExonArray.ra
- lines changed 119, context: html, text, full: html, text
updated metaDb for UWAffyExon, redmine# 59 note# 34
- src/hg/makeDb/trackDb/human/hg19/omimLocation.html
- lines changed 1, context: html, text, full: html, text
Updated human/hg19/omimLocation.html.
- src/hg/makeDb/trackDb/human/hg19/snp132ParTweak.html
- lines changed 13, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): At Brooke's suggestion, added a noteto the #Weight section about the tweaking of weights in the PAR region.
- src/hg/makeDb/trackDb/human/hg19/tfbsConsSites.html
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 100, context: html, text, full: html, text
Added a newly-reworked Affy Exon track
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
releasing the the sunyAlbany track with the corresponding super track, redmine issue# 460
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
- lines changed 1, context: html, text, full: html, text
Added the new elements data and some of the replacement data
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
- lines changed 61, context: html, text, full: html, text
Changed type from bedElements to bed6
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
- lines changed 10, context: html, text, full: html, text
Added a subheader and explained where you could get downloads
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
- lines changed 284, context: html, text, full: html, text
Changed to have the one with a treatment show as a cell type, for Tier 1 and Tier 2 to filter to the top
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
- lines changed 24, context: html, text, full: html, text
Removed the colors and the itemRGB
- lines changed 8, context: html, text, full: html, text
Cleaned up the meta data and the downloads display
- lines changed 6, context: html, text, full: html, text
Fixed long labels for six entries
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 18, context: html, text, full: html, text
Removed signal: wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep1 and wgEncodeHaibTfbsT47dCtcfV0416102Dmso2RawRep2, according to Flo.
- lines changed 508, context: html, text, full: html, text
Added 8 submissions that included missing data and resubmitted files with updated meta-data.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
- lines changed 11, context: html, text, full: html, text
Minute change to methods and links to genome-preview as cascade of open chrom composites are released.
- lines changed 5, context: html, text, full: html, text
Requested by Kate is explicit mention that replicates of alignments and raw data are available in downloads. Also noticed that downloads links should have been to hgFileUi
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
- lines changed 7, context: html, text, full: html, text
Minute change to methods and links to genome-preview as cascade of open chrom composites are released.
- lines changed 8, context: html, text, full: html, text
Requested by Kate is explicit mention that replicates of alignments and raw data are available in downloads. Also noticed that downloads links should have been to hgFileUi
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
- lines changed 9, context: html, text, full: html, text
Minute change to methods and links to genome-preview as cascade of open chrom composites are released.
- lines changed 8, context: html, text, full: html, text
Requested by Kate is explicit mention that replicates of alignments and raw data are available in downloads. Also noticed that downloads links should have been to hgFileUi
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
- lines changed 2, context: html, text, full: html, text
releasing the the sunyAlbany track with the corresponding super track, redmine issue# 460
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
- lines changed 2, context: html, text, full: html, text
Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.html
- lines changed 256, context: html, text, full: html, text
New description page, requires refs and contacts
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.ra
- lines changed 6, context: html, text, full: html, text
More 5C data agreement work
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
- lines changed 1, context: html, text, full: html, text
Changed windowing function from mean to mean+whiskers as requested by QA.
- lines changed 1, context: html, text, full: html, text
Added fileSortOrder to track.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
- lines changed 8, context: html, text, full: html, text
Changed the polyA+ to polyA- for K562
- src/hg/makeDb/trackDb/human/hg19Patch2/description.html
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 11, context: html, text, full: html, text
Added omimGene2 track to human/trackDb.ra.
- lines changed 19, context: html, text, full: html, text
Updated new OMIM tracks entries.
- src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
adding chain net overrides for all panTro3 related chain net combinations
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
- lines changed 2, context: html, text, full: html, text
Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
- lines changed 2, context: html, text, full: html, text
Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
- lines changed 2, context: html, text, full: html, text
Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html
- lines changed 2, context: html, text, full: html, text
Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html
- lines changed 2, context: html, text, full: html, text
Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
- lines changed 2, context: html, text, full: html, text
Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
- src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
- lines changed 5, context: html, text, full: html, text
adding chain net overrides for all panTro3 related chain net combinations
- src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
- lines changed 5, context: html, text, full: html, text
adding chain net overrides for all panTro3 related chain net combinations
- src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
adding chain net overrides for all panTro3 related chain net combinations
- src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
adding chain net overrides for all panTro3 related chain net combinations
- src/hg/makeDb/trackDb/snp132.shared.html
- lines changed 8, context: html, text, full: html, text
Added text at the top pointing out that the rest of the page is the same for all 4 snp132 tracks.
- lines changed 1, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): At Brooke's suggestion, added a noteto the #Weight section about the tweaking of weights in the PAR region.
- src/hg/makeDb/trackDb/turkey/melGal1/ctgPos2.html
- src/hg/makeDb/trackDb/turkey/melGal1/description.html
- lines changed 89, context: html, text, full: html, text
Edit turkey description page
- lines changed 56, context: html, text, full: html, text
Add html for gap, gold, and descrition
- src/hg/makeDb/trackDb/turkey/melGal1/gap.html
- lines changed 45, context: html, text, full: html, text
Add html for gap, gold, and descrition
- src/hg/makeDb/trackDb/turkey/melGal1/gold.html
- lines changed 13, context: html, text, full: html, text
Add html for gap, gold, and descrition
- src/hg/makeDb/trackDb/turkey/melGal1/trackDb.ra
- src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
- lines changed 16, context: html, text, full: html, text
adding chain net overrides for all panTro3 related chain net combinations
- src/hg/oneShot/doOmimAv/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/oneShot/dupedInTable/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/oneShot/kgName/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/oneShot/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/oneShot/musAliAt/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/oneShot/protDat/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/oneShot/testCart/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/oneShot/testTableExists/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/oneShot/weedKnownBlastTab/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/oneShot/weedTab/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/pslToFa/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/hg/qaPushQ/formPushQ.html
- lines changed 16, context: html, text, full: html, text
added new dropdown column "importance" with values from Redmine issue, as requested by Ann
- src/hg/qaPushQ/pushQ.as
- lines changed 1, context: html, text, full: html, text
added new dropdown column "importance" with values from Redmine issue, as requested by Ann
- src/hg/qaPushQ/pushQ.sql
- lines changed 52, context: html, text, full: html, text
this file was only added accidentally in recent months; it does not need to be in the source code since it is easily and automatically generated using autoSql in the makefile
- src/hg/qaPushQ/qaPushQ.c
- lines changed 34, context: html, text, full: html, text
added new dropdown column "importance" with values from Redmine issue, as requested by Ann
- src/hg/regulate/regClusterAttachMetadataToTableOfTables/makefile
- lines changed 18, context: html, text, full: html, text
Work on wgEncodeReg track.
- src/hg/regulate/regClusterAttachMetadataToTableOfTables/regClusterAttachMetadataToTableOfTables.c
- lines changed 177, context: html, text, full: html, text
Work on wgEncodeReg track.
- src/hg/regulate/regClusterBedExpCfg/cellLetter2.tab
- lines changed 95, context: html, text, full: html, text
More work on new TFBS clustering stuff.
- src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
- lines changed 147, context: html, text, full: html, text
Work on wgEncodeReg track.
- src/hg/regulate/regClusterTreeCells/makefile
- lines changed 18, context: html, text, full: html, text
First cut of cell clusterer. Runs and produces output, but output isn't making a bunch of sense. Need to develop some test cases.
- src/hg/regulate/regClusterTreeCells/regClusterTreeCells.c
- lines changed 349, context: html, text, full: html, text
First cut of cell clusterer. Runs and produces output, but output isn't making a bunch of sense. Need to develop some test cases.
- src/hg/utils/cpAndLinkToResourceFiles.pl
- lines changed 94, context: html, text, full: html, text
coallesce cpAndLinkToResourceFiles.pl
- lines changed 51, context: html, text, full: html, text
Use version based links in production sites, mtime based links in dev sites (see redmine #3170)
- src/hg/utils/refSeqGet/makefile
- lines changed 1, context: html, text, full: html, text
Recurse to tests in the clean target.
- src/inc/cheapcgi.h
- lines changed 9, context: html, text, full: html, text
Added lib routine for creating a single/multiple drop down, where the multiple will be expected to be converted into a ui-dropdownchecklist.js type multi-select
- src/inc/common.h
- lines changed 7, context: html, text, full: html, text
fixing processing of last-modified header in udc; also setting the original time on the finished file in paraFetch (net.c); new helper function in common.c handles conversion to UTC time
- src/inc/linefile.h
- lines changed 2, context: html, text, full: html, text
Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
- src/inc/vcf.h
- lines changed 181, context: html, text, full: html, text
Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
- src/jkOwnLib/genoFind.c
- lines changed 1, context: html, text, full: html, text
Bug #3150 (blat is crashing): The gfPepTile logic assumes that aaValcontains either -1 or 0 to 19. Previously, aaVal['X'] was -1. Then
in 1b5e64c4, 'X' was added to dnautil.c's aminoAcidTable and therefore
to aaVal, with aaVal['X'] = 20. One of the peptide test sequences
ends with "XXXXX", which caused gfPepTile to produce an out-of-range
tile, leading to a SEGV in gfStraightFindHits. Fix: if aaVal[] is > 19,
treat as if -1.
- src/lib/cheapcgi.c
- lines changed 74, context: html, text, full: html, text
Added lib routine for creating a single/multiple drop down, where the multiple will be expected to be converted into a ui-dropdownchecklist.js type multi-select
- src/lib/common.c
- lines changed 26, context: html, text, full: html, text
fixing processing of last-modified header in udc; also setting the original time on the finished file in paraFetch (net.c); new helper function in common.c handles conversion to UTC time
- src/lib/linefile.c
- lines changed 9, context: html, text, full: html, text
Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
- src/lib/makefile
- lines changed 1, context: html, text, full: html, text
Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
- src/lib/net.c
- lines changed 38, context: html, text, full: html, text
fixing processing of last-modified header in udc; also setting the original time on the finished file in paraFetch (net.c); new helper function in common.c handles conversion to UTC time
- src/lib/regexHelper.c
- lines changed 9, context: html, text, full: html, text
Build a more accurate description in regexMatchSubstrMaybeCase.
- src/lib/tests/expected/tabixFetch1kGNoGenotypes.out
- lines changed 6, context: html, text, full: html, text
Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
- src/lib/tests/expected/tabixFetch1kGWithGenotypes.out
- lines changed 7, context: html, text, full: html, text
Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
- src/lib/tests/expected/vcfParse1kGNoGenotypes.out
- lines changed 7, context: html, text, full: html, text
Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
- src/lib/tests/expected/vcfParse1kGWithGenotypes.out
- lines changed 8, context: html, text, full: html, text
Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
- src/lib/tests/input/YRI.low_coverage.2010_07_excerpt.genotypes.vcf.gz
- lines changed 0, context: html, text, full: html, text
Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
- src/lib/tests/input/YRI.low_coverage.2010_07_excerpt.genotypes.vcf.gz.tbi
- lines changed 0, context: html, text, full: html, text
Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
- src/lib/tests/input/YRI.trio.2010_06.novelsequences.sites.vcf.gz
- lines changed 0, context: html, text, full: html, text
Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
- src/lib/tests/input/YRI.trio.2010_06.novelsequences.sites.vcf.gz.tbi
- lines changed 0, context: html, text, full: html, text
Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
- src/lib/tests/makefile
- lines changed 37, context: html, text, full: html, text
Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
- src/lib/tests/tabixFetch.c
- lines changed 114, context: html, text, full: html, text
Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/.
Test cases coming up...
- lines changed 1, context: html, text, full: html, text
Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
- src/lib/tests/vcfParseTest.c
- lines changed 56, context: html, text, full: html, text
Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/.
Test cases coming up...
- src/lib/udc.c
- lines changed 6, context: html, text, full: html, text
fixing processing of last-modified header in udc; also setting the original time on the finished file in paraFetch (net.c); new helper function in common.c handles conversion to UTC time
- src/lib/vcf.c
- lines changed 767, context: html, text, full: html, text
Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
- lines changed 8, context: html, text, full: html, text
Feature #2821 (VCF parser): adding workaround for annoying non-ASCIIcharacters in the header of a file included in 1000 Genomes' pilot
release, found when adding basic test case.
- src/oneShot/balancedTree/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/oneShot/findContigsWithClones/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/oneShot/foo2/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/oneShot/formatFastaSeq/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/oneShot/mafFindZero/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/oneShot/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/oneShot/newStitch4/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/oneShot/tabixFetch/makefile
- lines changed 18, context: html, text, full: html, text
Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/.
Test cases coming up...
- src/oneShot/tabixFetch/tabixFetch.c
- lines changed 114, context: html, text, full: html, text
Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/.
Test cases coming up...
- src/oneShot/test/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/oneShot/vcfParseTest/makefile
- lines changed 18, context: html, text, full: html, text
Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
- lines changed 18, context: html, text, full: html, text
Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/.
Test cases coming up...
- src/oneShot/vcfParseTest/vcfParseTest.c
- lines changed 56, context: html, text, full: html, text
Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
- lines changed 56, context: html, text, full: html, text
Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/.
Test cases coming up...
- src/parasol/dataSim/makefile
- lines changed 1, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/parasol/para/para.c
- lines changed 2, context: html, text, full: html, text
Doubling max queue size since we seem to actually sometimes be hitting limit and memory has more than doubled since this was set.
- src/product/scripts/fetchMinimalGbdb.sh
- lines changed 4, context: html, text, full: html, text
update to include trix and metaDb files and properly rsync js and style directories
- src/product/scripts/fetchMinimalGoldenPath.sh
- lines changed 2, context: html, text, full: html, text
update to include trix and metaDb files and properly rsync js and style directories
- src/product/scripts/updateHtml.sh
- lines changed 6, context: html, text, full: html, text
update to include trix and metaDb files and properly rsync js and style directories
- src/reformat/makeOrf2gene/makefile
- lines changed 2, context: html, text, full: html, text
eliminate use of HOME in MYLIBDIR
- src/utils/bigBedSummary/makefile
- lines changed 1, context: html, text, full: html, text
properly clean the executable
- src/utils/bigBedToBed/makefile
- lines changed 1, context: html, text, full: html, text
properly clean the executable
- src/utils/bigWigSummary/makefile
- lines changed 1, context: html, text, full: html, text
properly clean the executable
- src/utils/bigWigToBedGraph/makefile
- lines changed 1, context: html, text, full: html, text
properly clean the executable
- src/utils/git-reports/git-reports.c
- lines changed 1, context: html, text, full: html, text
adding note that 0 lines diff happens with binary files too
- src/utils/makefile
- lines changed 6, context: html, text, full: html, text
this clean target wasn't descending into USE_DIRS
- lines changed 1, context: html, text, full: html, text
properly clean the executable
- src/utils/qa/alertBqueue.csh
- lines changed 1, context: html, text, full: html, text
corrected donna's email address
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 20291
- files changed: 322