All File Changes
v272_preview to v272_preview2 (2012-08-14 to 2012-08-21) v272
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 1, context: html, text, full: html, text
removed need for dataBrowser
- src/hg/hgSuggest/hgSuggest.c
- lines changed 2, context: html, text, full: html, text
add missing clause in like to fix problem with exact queries in non-knowGene assemblies (see #8807)
- lines changed 13, context: html, text, full: html, text
use correct name for refGene internal_id name; break up long lines per angie's code review
- src/hg/hgTables/bigBed.c
- lines changed 58, context: html, text, full: html, text
fixed #8834 by querying only part of the chrom to get ten items for schema
- src/hg/hgTracks/gencodeTracks.c
- lines changed 21, context: html, text, full: html, text
fixed crash accessing 2way consensus pseudogenes because they don't have the extended genePred field
- lines changed 1, context: html, text, full: html, text
removed extra call to genePredAssignConfiguredName that did nothing
- src/hg/hgTracks/menu.c
- lines changed 1, context: html, text, full: html, text
Added text, (Convert), after 'in other Genomes' since this was previously labelled convert. Also changed casing or words to standard grammar since whether to capitalize all words or not is in the css. Leaves more flexibility to the css.
- src/hg/hgc/bigBedClick.c
- lines changed 31, context: html, text, full: html, text
display multiples for bigBed when more than one record share exactly the same chrom, start, end, and name
- src/hg/hgc/encodeClick.c
- lines changed 11, context: html, text, full: html, text
fix hgc/encodeClick doEncodePeak to support items and use them to match unique display - even though multiples are now incredibly rare with new item=name matching, the code improves the display of the multiples by separating them with a vertical space
- src/hg/hgc/hgc.c
- lines changed 2, context: html, text, full: html, text
fix hgc/encodeClick doEncodePeak to support items and use them to match unique display - even though multiples are now incredibly rare with new item=name matching, the code improves the display of the multiples by separating them with a vertical space
- lines changed 2, context: html, text, full: html, text
display multiples for bigBed when more than one record share exactly the same chrom, start, end, and name
- src/hg/hgc/hgc.h
- lines changed 1, context: html, text, full: html, text
fix hgc/encodeClick doEncodePeak to support items and use them to match unique display - even though multiples are now incredibly rare with new item=name matching, the code improves the display of the multiples by separating them with a vertical space
- lines changed 1, context: html, text, full: html, text
display multiples for bigBed when more than one record share exactly the same chrom, start, end, and name
- src/hg/htdocs/ENCODE/downloadsMouse.html
- lines changed 2, context: html, text, full: html, text
Correcting labels for link added to ENCODE mouse download page for PSU RNA-seq (Release 1) RM#107
- lines changed 4, context: html, text, full: html, text
Adding link for ENCODE mouse downloads for PSU DNase (Release 1) RM#109
- src/hg/htdocs/FAQ/FAQreleases.html
- src/hg/htdocs/goldenPath/credits.html
- lines changed 45, context: html, text, full: html, text
Added Medium ground finch to credits. It still needs a link to use restrictions.
- lines changed 22, context: html, text, full: html, text
Updated use restrictions for Medium ground finch.
- lines changed 2, context: html, text, full: html, text
Opps, copy and pasted some text from opossum and didn't change the references for Medium ground finch. Done.
- src/hg/htdocs/goldenPath/help/mysql.html
- lines changed 1, context: html, text, full: html, text
Changed link per code review feedback.
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 61, context: html, text, full: html, text
Added news item on Medium ground finch and archived some items.
- src/hg/htdocs/inc/globalNavBar.inc
- lines changed 1, context: html, text, full: html, text
Removed Help link to Mirrors, as we added a whole pulldown for Mirrors info, so it seemed redundant.
- lines changed 3, context: html, text, full: html, text
changed references to .cse. to .soe.
- src/hg/htdocs/inc/topbar.html
- lines changed 0, context: html, text, full: html, text
Changed url reference from .cse. to .soe.; redmine #8831.
- src/hg/htdocs/index.html
- lines changed 3, context: html, text, full: html, text
Changed .cse. to .soe. in url, fixed a couple html bugs.
- src/hg/htdocs/indexNews.html
- lines changed 24, context: html, text, full: html, text
Added story about new browser look and feel
- lines changed 2, context: html, text, full: html, text
fixed link to go to genome.ucsc
- lines changed 106, context: html, text, full: html, text
Added news item on Medium ground finch and archived some items.
- src/hg/htdocs/makefile
- lines changed 6, context: html, text, full: html, text
allow overriding CGI_BIN user directory and htdocs in environment
- src/hg/lib/hdb.c
- lines changed 5, context: html, text, full: html, text
fix #8796. Hub tracks don't have a tdb in the track hash, so we shouldn't expect to find one there.
- lines changed 39, context: html, text, full: html, text
more changes to support UCSC genes (#7045). Added script to build new proteome database, fixed some utilities used in the building of that database, removed dependency on gdbPdb table in hgcentral (now it just uses the most recent proteome database rather than having a proteins database per assembly)
- src/hg/makeDb/doc/encodeDccHg19/gencodeV12.txt
- src/hg/makeDb/doc/encodeDccHg19/gencodeV13.txt
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release3.notes
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release3.notes
- lines changed 4734, context: html, text, full: html, text
added in notes for sydh tfbs
- lines changed 59, context: html, text, full: html, text
added in supplemental files in notes
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeCshlLongRnaSeq.release3.notes
- lines changed 1569, context: html, text, full: html, text
First draft of notes file, I think the replace did not work
- lines changed 91, context: html, text, full: html, text
Added in supplemental and the renames for some of the V2s
- lines changed 11, context: html, text, full: html, text
Adding readme and files.txt
- src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuDnase.release1.notes
- lines changed 73, context: html, text, full: html, text
Added release notes for release 1 of dataset. Redmine #109.
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhHist.release2.notes
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release4.notes
- lines changed 1035, context: html, text, full: html, text
added in sydh tfbs mm9 notes first draft
- src/hg/makeDb/doc/geoFor1.txt
- lines changed 1, context: html, text, full: html, text
add a time result from exonNuc.fa.gz construction
- src/hg/makeDb/doc/mm10.txt
- lines changed 74, context: html, text, full: html, text
rerun the 4D phyloFit with the new groupings
- src/hg/makeDb/doc/proteins/120806.txt
- lines changed 693, context: html, text, full: html, text
more changes to support UCSC genes (#7045). Added script to build new proteome database, fixed some utilities used in the building of that database, removed dependency on gdbPdb table in hgcentral (now it just uses the most recent proteome database rather than having a proteins database per assembly)
- src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
- lines changed 4, context: html, text, full: html, text
more changes to support UCSC genes (#7045). Added script to build new proteome database, fixed some utilities used in the building of that database, removed dependency on gdbPdb table in hgcentral (now it just uses the most recent proteome database rather than having a proteins database per assembly)
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 2, context: html, text, full: html, text
use ensembl genes instead of refGene for the upstream files because there's no UTR defined for the refGene models
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- lines changed 14, context: html, text, full: html, text
Added 14 almost-archived assemblies back to the list. See http://redmine.soe.ucsc.edu/issues/698#note-35.
- src/hg/makeDb/genbank/etc/rr.dbs
- lines changed 1, context: html, text, full: html, text
Added geoFor1 assembly to list. Releasing in a couple of days.
- lines changed 14, context: html, text, full: html, text
Added 14 almost-archived assemblies back to the list. See http://redmine.soe.ucsc.edu/issues/698#note-35.
- src/hg/makeDb/genbank/makefile
- lines changed 1, context: html, text, full: html, text
fix up makefile to build libraries before executables with target install-rr
- src/hg/makeDb/hgTrackDb/hgTrackDb.c
- lines changed 10, context: html, text, full: html, text
Renamed dsprint to dyOut. Hopefully this proves to be a more popular name.
- src/hg/makeDb/trackDb/alpaca/vicPac1/trackDb.ra
- lines changed 7, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/armadillo/dasNov3/trackDb.ra
- lines changed 8, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/baboon/papAnu2/description.html
- lines changed 1, context: html, text, full: html, text
Fix the wrong picture problem.
- src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
- lines changed 1, context: html, text, full: html, text
update vertebrate.mod hgdownload reference
- src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra
- lines changed 8, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra
- lines changed 8, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra
- lines changed 7, context: html, text, full: html, text
update gold track frag search rule
- lines changed 1, context: html, text, full: html, text
better regex specification to catch all frag names
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 973, context: html, text, full: html, text
Alphabetizing a set of antibodies in CV
- lines changed 1, context: html, text, full: html, text
Fixed some strain designations.
- lines changed 16, context: html, text, full: html, text
Fixing up some labels in the CV
- lines changed 4, context: html, text, full: html, text
Testing label change in CV and wiki
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 2, context: html, text, full: html, text
Fixing target for REST antibody
- lines changed 1347, context: html, text, full: html, text
Copying alpha cv to beta
- lines changed 30, context: html, text, full: html, text
Pushing some fixes from alpha cv to beta
- src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra
- lines changed 8, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/gadMor/gadMor1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/gibbon/nomLeu2/trackDb.ra
- lines changed 8, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/hedgehog/eriEur1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/human/hg19/altSeqComposite9.ra
- lines changed 1, context: html, text, full: html, text
Undid changes I made previously; Hiram's changes went out with today's CGI release, so the altSeqLiftOverPsl table can have the 'P9' added back and it will no longer interfere with the Patch 5 track (redmine #7195)
- src/hg/makeDb/trackDb/human/hg19/description.html
- lines changed 1, context: html, text, full: html, text
Updated link as per MLQ #8799.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylWgbs.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- lines changed 553, context: html, text, full: html, text
added in new open chrom tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 41, context: html, text, full: html, text
renaming antibody to proper name
- lines changed 203, context: html, text, full: html, text
removed duplicate experiement, added md5sums
- lines changed 524, context: html, text, full: html, text
added in EpxIDs and missing controls
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhTfbs.ra
- lines changed 7306, context: html, text, full: html, text
Staging on beta Stanford Yale TFBS (Release 3) RM#7827
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisRnaPet.ra
- lines changed 4558, context: html, text, full: html, text
Staging on public, GIS RNA PET (Release 2) RM#5942
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhTfbs.ra
- lines changed 7306, context: html, text, full: html, text
Staging on public Stanford Yale TFBS (Release 3) RM#7827
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Undid changes I made previously; Hiram's changes went out with today's CGI release, so the altSeqLiftOverPsl table can have the 'P9' added back and it will no longer interfere with the Patch 5 track (redmine #7195)
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Staging on public, GIS RNA PET (Release 2) RM#5942
- lines changed 8, context: html, text, full: html, text
Updated release tags to make new highlighting feature available on the RR (redmine #8634)
- lines changed 8, context: html, text, full: html, text
A bug was discovered in conjunction with the GENCODE highlighting feature; putting it back on beta for the moment (redmine #8634)
- lines changed 8, context: html, text, full: html, text
Re-enabling the GENCODE highlighting feature... again... (redmine #8634)
- lines changed 2, context: html, text, full: html, text
Staging on beta Stanford Yale TFBS (Release 3) RM#7827
- lines changed 2, context: html, text, full: html, text
Staging on public Stanford Yale TFBS (Release 3) RM#7827
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.ra
- lines changed 227, context: html, text, full: html, text
added fogotten V13.ra file
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.html
- lines changed 19, context: html, text, full: html, text
Adding notes about the porr scores and disabling score usage
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
- lines changed 1, context: html, text, full: html, text
Adding notes about the porr scores and disabling score usage
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.html
- lines changed 16, context: html, text, full: html, text
changed the html page for HAIB WGBS to fix errors Steve found during QA
- lines changed 4, context: html, text, full: html, text
fixed the release notes and added link to bowtie for HAIB WGBS
- lines changed 5, context: html, text, full: html, text
made some additional changes that Steve noticed for this track
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.ra
- lines changed 9, context: html, text, full: html, text
Small changes in labels and defaults for ticket #6770
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release3.ra
- lines changed 107, context: html, text, full: html, text
adding in trackDb tracks for openchnrom Dnase
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.ra
- lines changed 8, context: html, text, full: html, text
renaming antibody to proper name
- lines changed 16, context: html, text, full: html, text
removing duplicate experiment
- lines changed 8, context: html, text, full: html, text
added in EpxIDs and missing controls
- lines changed 102, context: html, text, full: html, text
first pass at new short labels
- lines changed 1, context: html, text, full: html, text
removing default on configuration box
- lines changed 825, context: html, text, full: html, text
qa fixes including alphabetization, and labels
- lines changed 1, context: html, text, full: html, text
one more UCDavis -> UC Davis
- lines changed 1, context: html, text, full: html, text
moved znf 263 to correct place
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.ra
- lines changed 2, context: html, text, full: html, text
fix order in matrix in responding to Brian's note 67, #8419
- src/hg/makeDb/trackDb/kangarooRat/dipOrd1/trackDb.ra
- lines changed 7, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra
- lines changed 7, context: html, text, full: html, text
update gold track frag search rule
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
- lines changed 3, context: html, text, full: html, text
Reordered organisms to match the order in the phylo tree image. Tree shrew is currently part of the glire group for phastcons and phyloP; waiting to see if we are going to change that before moving it here.
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
- lines changed 1, context: html, text, full: html, text
add special note about geoFor1
- src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html
- lines changed 191, context: html, text, full: html, text
add special note about geoFor1
- lines changed 19, context: html, text, full: html, text
Cleaned up some html and made the table and list look nicer.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 53, context: html, text, full: html, text
Giving accession numbers for the spikeins
- lines changed 192, context: html, text, full: html, text
part of the double compression fix, this fix was for mm9 cshl
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
- lines changed 28, context: html, text, full: html, text
filled in missing controls
- lines changed 220, context: html, text, full: html, text
added in missing controls
- lines changed 28, context: html, text, full: html, text
adding in expIds and accessions
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 133, context: html, text, full: html, text
filled in missing controls
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 237, context: html, text, full: html, text
update with new dataset
- lines changed 71, context: html, text, full: html, text
Updated md5sum's. Redmine #4468.
- lines changed 46, context: html, text, full: html, text
Changed rename to renamed and shortened message to not have special chars. This was confusing metacheck
- lines changed 22, context: html, text, full: html, text
Added strain to expVars so that 3 experiments on Liver E18.5 cells could be differentiated. Redmine #4468.
- lines changed 222, context: html, text, full: html, text
Fixed naming of V2 of objects for ZhBTc4 that were resubmitted but had the wrong sex. Added objStatus to old submissions. Redmine #4468.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
Staging beta mm9 PSU Dnase (Release 1/Final) RM#109
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
- lines changed 9916, context: html, text, full: html, text
part of the double compression fix, this fix was for mm9 cshl
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuDnase.ra
- lines changed 398, context: html, text, full: html, text
Staging beta mm9 PSU Dnase (Release 1/Final) RM#109
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhHist.ra
- lines changed 2236, context: html, text, full: html, text
Staging SYDH Histone (Release 2) on beta (redmine #5404)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhTfbs.ra
- lines changed 3316, context: html, text, full: html, text
Staging on beta, Stanford Yale TFBS (Release 4) RM#7981
- lines changed 265, context: html, text, full: html, text
Restaging on beta Stanford Yale TFBS (Release 4) RM#7981 to update metadata
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
Staging on public PSU DNase (Release 1/Final) RM#109
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuDnase.ra
- lines changed 398, context: html, text, full: html, text
Staging on public PSU DNase (Release 1/Final) RM#109
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhHist.ra
- lines changed 2236, context: html, text, full: html, text
Releasing SYDH Histone (Release 2) to the RR (redmine #5404)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhTfbs.ra
- lines changed 3580, context: html, text, full: html, text
Staging public for Standford Yale TFBS (Release 4) RM# 7981
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
replaced trackDb with release 4 for sydh tfbs
- lines changed 2, context: html, text, full: html, text
Staging on beta, Stanford Yale TFBS (Release 4) RM#7981
- lines changed 2, context: html, text, full: html, text
Staging public for Standford Yale TFBS (Release 4) RM# 7981
- lines changed 2, context: html, text, full: html, text
Staging SYDH Histone (Release 2) on beta (redmine #5404)
- lines changed 2, context: html, text, full: html, text
Releasing SYDH Histone (Release 2) to the RR (redmine #5404)
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release3.ra
- lines changed 656, context: html, text, full: html, text
Mostly long and short label changes, removing all of the V1 data for the alignments
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuDnase.html
- lines changed 100, context: html, text, full: html, text
Added track Description. Redmine #109.
- lines changed 3, context: html, text, full: html, text
Changes for Redmine #109
Q1. Cgabged called to identified
Q3. Updated sentence to use rather and not but
Q4. Added the to sentence
- lines changed 1, context: html, text, full: html, text
Correcting typo for PSU DNase (Release 1/Final) RM#109
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.html
- lines changed 5, context: html, text, full: html, text
Fixed typo in credits section.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.html
- lines changed 1, context: html, text, full: html, text
adding SYDH tag to the html file, hopefully it fools track search
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra
- lines changed 28, context: html, text, full: html, text
added in missing controls
- lines changed 14, context: html, text, full: html, text
changed some short labels around
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
- lines changed 439, context: html, text, full: html, text
restoring to old trackDb for release
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release4.html
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release4.ra
- lines changed 1167, context: html, text, full: html, text
adding in release 4 sydh tfbs trackDb initial
- lines changed 439, context: html, text, full: html, text
applying changes made to release3 to release4, for a proper release split
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
- lines changed 86, context: html, text, full: html, text
update with new datasets
- lines changed 1, context: html, text, full: html, text
Revert "change CH12 order"
This reverts commit 591237cefaf980b1b84ff87b2ceb9ae0a517f67a.
•
• modified: src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
this file is an old release, need to revert the update which was meaned for the new release#
Untracked files:
(use "git add <file>..." to include in what will be committed)
- lines changed 6, context: html, text, full: html, text
Revert "turn on CH12 display"
This reverts commit 135d5348255920bfed44e0cceabfc0ce62fbf00a.
new dataset was accidently added to this old release
- lines changed 86, context: html, text, full: html, text
Revert "update with new datasets"
This reverts commit 19876e7a81f5e6732321b635a8180a197b812190.
new dataset was updated in this old release, it should have been done in the new release
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
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copy over the update for the new datasets from the old release file
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update all the existing dataset with treatment var
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Reverts commits: b912549a8ffa41615f1c72d646ae32f88b56c8d8 and c6168a81d1fb9bee0512eb6ef38f35cd406543ac, where wrangler copied over file from release1 that trampled changes that were unique to release2. Redmine #4468.
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Added in CH12 datasets that were miss handled before. Redmine #4468.
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First pass at some label fixing. Redmine #4468.
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Updated some more labels. Redmine #4468.
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Added strain as a filterby composite. Redmine #4468.
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Fixed naming of V2 of objects for ZhBTc4 that were resubmitted but had the wrong sex. Added objStatus to old submissions. Redmine #4468.
- src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra
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update gold track frag search rule
- src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra
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update gold track frag search rule
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better regex specification to catch all frag names
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fixup genscan table search rules
- src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
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fixup ensGen protein search rule to avoid errors in checkHgFindSpec redmine 5727
- src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
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update gold track frag search rule
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fixup genscan table search rules
- src/hg/makeDb/trackDb/pika/ochPri2/trackDb.ra
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update gold track frag search rule
- src/hg/makeDb/trackDb/rat/rn3/trackDb.ra
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fixup search rule to avoid errors in checkHgFindSpec redmine 5727
- src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
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fixup search rule to avoid errors in checkHgFindSpec redmine 5727
- src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
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update gold track frag search rule
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better regex specification to catch all frag names
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fixup genscan table search rules
- src/hg/makeDb/trackDb/rockHyrax/proCap1/trackDb.ra
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update gold track frag search rule
- src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
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fixup ensGen protein search rule to avoid errors in checkHgFindSpec redmine 5727
- src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
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update gold track frag search rule
- src/hg/makeDb/trackDb/shrew/sorAra1/trackDb.ra
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update gold track frag search rule
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update gold track frag search rule
- src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra
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update gold track frag search rule
- src/hg/makeDb/trackDb/tarsier/tarSyr1/trackDb.ra
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update gold track frag search rule
- src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/trackDb.ra
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update gold track frag search rule
- src/hg/makeDb/trackDb/tetraodon/tetNig1/trackDb.ra
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fixup ensGen protein search rule to avoid errors in checkHgFindSpec redmine 5727
- src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra
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better regex specification to catch all frag names
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fixup genscan table search rules
- src/hg/protein/pbHgnc/pbHgnc.c
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more changes to support UCSC genes (#7045). Added script to build new proteome database, fixed some utilities used in the building of that database, removed dependency on gdbPdb table in hgcentral (now it just uses the most recent proteome database rather than having a proteins database per assembly)
- src/hg/protein/spToSpXref2/spToSpXref2.c
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more changes to support UCSC genes (#7045). Added script to build new proteome database, fixed some utilities used in the building of that database, removed dependency on gdbPdb table in hgcentral (now it just uses the most recent proteome database rather than having a proteins database per assembly)
- src/hg/utils/automation/EnsGeneAutomate.pm
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remove broken illegal comment
- src/hg/utils/automation/doBlastzChainNet.pl
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bug in default BLASTZ_L value, redmine 5796 and 5882
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bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
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- src/utils/bedPileUps/tests/expected/foo2.bed.txt
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bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
- src/utils/bedPileUps/tests/expected/foo3.bed.txt
- lines changed 3, context: html, text, full: html, text
bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
- src/utils/bedPileUps/tests/expected/foo4.bed.txt
- lines changed 3, context: html, text, full: html, text
bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
- src/utils/bedPileUps/tests/input/foo.bed
- lines changed 42, context: html, text, full: html, text
bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
- src/utils/bedPileUps/tests/input/foo2.bed
- lines changed 21, context: html, text, full: html, text
bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
- src/utils/bedPileUps/tests/input/foo3.bed
- lines changed 103, context: html, text, full: html, text
bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
- src/utils/bedPileUps/tests/input/foo4.bed
- lines changed 206, context: html, text, full: html, text
bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
- src/utils/makefile
- lines changed 1, context: html, text, full: html, text
bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 69745
- files changed: 349