CVS changes by file

review to branch (2009-10-06 to 2009-10-13) v217

• src/blat/blat.c
  • 1.115 lines changed: 1, context: html, text, full: html, text
    Making sure stepSize is initialized
  • 1.114 lines changed: 45, context: html, text, full: html, text
    Moving repMatch calculations from blat to library so can be shared with gfServer.
• src/blat/version.doc
  • 1.74 lines changed: 2, context: html, text, full: html, text
    Moving repMatch calculations from blat to library so can be shared with gfServer.
• src/gfServer/gfServer.c
  • 1.57 lines changed: 3, context: html, text, full: html, text
    Trimming a few lines to make it follow same stepSize pattern as blat.c
  • 1.56 lines changed: 5, context: html, text, full: html, text
    Moving repMatch calculations from blat to library so can be shared with gfServer.
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.86 lines changed: 33, context: html, text, full: html, text
    add haloVolc1_1 from Halolex
• src/hg/archaeStuff/data/private-genomes.tab
  • 1.3 lines changed: 16, context: html, text, full: html, text
    add haloferax private browser and haloVolc1_1 as private genome
  • 1.2 lines changed: 14, context: html, text, full: html, text
    mark all private genomes as private to haloferax collab browser
• src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm
  • 1.26 lines changed: 21, context: html, text, full: html, text
    make more coding changes to support annotRev in Blastp
  • 1.25 lines changed: 36, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
  • 1.24 lines changed: 158, context: html, text, full: html, text
    read private-genomes.tab to skip sync'ing and initdb; add --removepriv to clean up hits to private genomes in blastp, blastx, and alignFeatures tracks
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.20 lines changed: 35, context: html, text, full: html, text
    make more coding changes to support annotRev in Blastp
  • 1.19 lines changed: 325, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.37 lines changed: 4, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
  • 1.36 lines changed: 72, context: html, text, full: html, text
    read private-genomes.tab to skip sync'ing and initdb; add --removepriv to clean up hits to private genomes in blastp, blastx, and alignFeatures tracks
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.45 lines changed: 3, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
  • 1.44 lines changed: 102, context: html, text, full: html, text
    read private-genomes.tab to skip sync'ing and initdb; add --removepriv to clean up hits to private genomes in blastp, blastx, and alignFeatures tracks
• src/hg/archaeStuff/scripts/archaeBrowser/RemovePriv.pm
  • 1.2 lines changed: 2, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
  • 1.1 lines changed: 196, context: html, text, full: html, text
    add -removepriv to clean up private genome hits
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.50 lines changed: 5, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
  • 1.49 lines changed: 11, context: html, text, full: html, text
    read private-genomes.tab to skip sync'ing and initdb; add --removepriv to clean up hits to private genomes in blastp, blastx, and alignFeatures tracks
• src/hg/bedSplitOnChrom/bedSplitOnChrom.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    put tabs between bed fields
• src/hg/encode/DAFs/UMassTfbsAll.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add new required setting
• src/hg/encode/DAFs/UMassTfbsValid.daf
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Add new required setting
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.134 lines changed: 1, context: html, text, full: html, text
    Changed BJ-tert to BJ by Stam lab request.
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.21 lines changed: 5, context: html, text, full: html, text
    Add support for specifying track group in DAF
• src/hg/encode/encodeValidate/config/labs.ra
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Replace Andy's entries
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.200 lines changed: 7, context: html, text, full: html, text
    Add color by cell type (from cv.ra) to trackDb file
  • 1.199 lines changed: 3, context: html, text, full: html, text
    Allow metadata extraction w/o requiring file validation settings, for backwards compatibility
  • 1.198 lines changed: 3, context: html, text, full: html, text
    make validationSettings required
  • 1.197 lines changed: 5, context: html, text, full: html, text
    Add support for specifying track group in DAF
• src/hg/encode/encodeValidate/test/expected/chipseq/README.txt
  • 1.5 lines changed: 9, context: html, text, full: html, text
    Add testing of color by cell type from cv.ra
  • 1.4 lines changed: 6, context: html, text, full: html, text
    Change name of chipseq test so it differs from real track so it can test out composite trackDb output
• src/hg/encode/encodeValidate/test/expected/chipseq/load.ra
  • 1.6 lines changed: 10, context: html, text, full: html, text
    Add testing of color by cell type from cv.ra
  • 1.5 lines changed: 5, context: html, text, full: html, text
    Change name of chipseq test so it differs from real track so it can test out composite trackDb output
• src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra
  • 1.8 lines changed: 21, context: html, text, full: html, text
    Add testing of color by cell type from cv.ra
  • 1.7 lines changed: 28, context: html, text, full: html, text
    Change name of chipseq test so it differs from real track so it can test out composite trackDb output
  • 1.6 lines changed: 30, context: html, text, full: html, text
    Update chipseq tests for latest DAF & label conventions. Assure they fail if expected files differ. Disable methylseq test for now.
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip-Test-Jun08.DDF
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Add testing of color by cell type from cv.ra
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip.DAF
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Change name of chipseq test so it differs from real track so it can test out composite trackDb output
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Update chipseq tests for latest DAF & label conventions. Assure they fail if expected files differ. Disable methylseq test for now.
• src/hg/encode/encodeValidate/test/makefile
  • 1.24 lines changed: 7, context: html, text, full: html, text
    Update chipseq tests for latest DAF & label conventions. Assure they fail if expected files differ. Disable methylseq test for now.
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • 1.17 lines changed: 6, context: html, text, full: html, text
    help in the concurrency battle with validator or loader mods to projects record
• src/hg/encode/hgEncodeSubmit/pipeline_runner.rb
  • 1.5 lines changed: 1, context: html, text, full: html, text
    local vars are undefined, not nil like $global and @instance
• src/hg/hgGene/makefile
  • 1.39 lines changed: 1, context: html, text, full: html, text
    fixup install target so files go to correct hgGeneData on 'make install'
• src/hg/hgGenome/bedList.c
  • 1.5 lines changed: 40, context: html, text, full: html, text
    getting it to be a little more consistent, better code organization, and fixes problem where custom bedGraph track was not working
  • 1.4 lines changed: 13, context: html, text, full: html, text
    added support for customtrack to getBedGraphField
• src/hg/hgGenome/hgGenome.h
  • 1.38 lines changed: 14, context: html, text, full: html, text
    getting it to be a little more consistent, better code organization, and fixes problem where custom bedGraph track was not working
• src/hg/hgGenome/import.c
  • 1.16 lines changed: 44, context: html, text, full: html, text
    getting it to be a little more consistent, better code organization, and fixes problem where custom bedGraph track was not working
• src/hg/hgTracks/bamTrack.c
  • 1.10 lines changed: 9, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/hgTracks/hgTracks.c
  • 1.1601 lines changed: 13, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/hgTracks/makefile
  • 1.88 lines changed: 3, context: html, text, full: html, text
    Use of samtools is spreading in the tree, so (if USE_BAM) add SAMLIB to L at the top level (inc/common.mk).
• src/hg/hgc/bamClick.c
  • 1.11 lines changed: 11, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/hgc/hgc.c
  • 1.1578 lines changed: 4, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/hgc/makefile
  • 1.64 lines changed: 3, context: html, text, full: html, text
    Use of samtools is spreading in the tree, so (if USE_BAM) add SAMLIB to L at the top level (inc/common.mk).
• src/hg/inc/bamFile.h
  • 1.11 lines changed: 3, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/inc/versionInfo.h
  • 1.157 lines changed: 1, context: html, text, full: html, text
    "New version number v217"
• src/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.77 lines changed: 5, context: html, text, full: html, text
    
  • 1.76 lines changed: 11, context: html, text, full: html, text
    single subgroup drawing functionality under summery view
• src/hg/instinct/hgHeatmap2/hgHeatmap2.c
  • 1.79 lines changed: 10, context: html, text, full: html, text
    
  • 1.78 lines changed: 15, context: html, text, full: html, text
    single subgroup drawing functionality under summery view
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_chin2006.ra
  • 1.4 lines changed: 21, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenMinGBMBio.ra
  • 1.3 lines changed: 12, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenMinOVBio.ra
  • 1.3 lines changed: 12, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_lajos.ra
  • 1.6 lines changed: 1, context: html, text, full: html, text
    
  • 1.5 lines changed: 107, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_vijver2002.ra
  • 1.4 lines changed: 58, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
  • 1.20 lines changed: 1, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAopen.ra
  • 1.7 lines changed: 3, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.28 lines changed: 28, context: html, text, full: html, text
    updated cosmic data
  • 1.27 lines changed: 3, context: html, text, full: html, text
    
  • 1.26 lines changed: 1, context: html, text, full: html, text
    single subgroup drawing functionality under summery view
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
  • 1.75 lines changed: 3, context: html, text, full: html, text
    
  • 1.74 lines changed: 37, context: html, text, full: html, text
    single subgroup drawing functionality under summery view
• src/hg/instinct/lib/hgHeatmapLib.c
  • 1.62 lines changed: 5, context: html, text, full: html, text
    
• src/hg/js/hui.js
  • 1.37 lines changed: 4, context: html, text, full: html, text
    Fixed bug that broke IE8 support. Problem was that IE* doesn't support local variable 'class' and instead tries to overwrite obj.class.
  • 1.36 lines changed: 14, context: html, text, full: html, text
    Fixed some 3D matrix plus-minus button problems.
• src/hg/lib/alignInfo.sql
  • 1.1 lines changed: 21, context: html, text, full: html, text
    created by Andrew Holmes for lowelab alignment feature track
• src/hg/lib/bamFile.c
  • 1.10 lines changed: 17, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/lib/customFactory.c
  • 1.106 lines changed: 41, context: html, text, full: html, text
    Added support for bam as a custom track type.
  • 1.105 lines changed: 68, context: html, text, full: html, text
    A little code cleanup: removed vestigial save/restore of env vars, improved a couple warning messages, replaced dangerous use of stack variable outside its scope w/dyString, removed some unnecessary uses of dyString.
• src/hg/lib/hdb.c
  • 1.416 lines changed: 3, context: html, text, full: html, text
    use sqlTableExists() in place of hTableExists() to avoid custom track bottleneck
• src/hg/lib/hgConfig.c
  • 1.22 lines changed: 3, context: html, text, full: html, text
    Don't require user-read-only for included files (just ~/.hg.conf itself). This allows us to include our cgi-bin-\angie/hg.conf files, and simply override the db.user and password in ~/.hg.conf.
• src/hg/lib/pgSnp.sql
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixed INDEX.
• src/hg/makeDb/doc/danRer6.txt
  • 1.11 lines changed: 25, context: html, text, full: html, text
    adding to the pushQ and all.joiner
  • 1.10 lines changed: 1, context: html, text, full: html, text
    its done
• src/hg/makeDb/doc/encodeDccHg18/yaleUpdate9-30.notes.txt
  • 1.2 lines changed: 556, context: html, text, full: html, text
    Added 5 more submissions included in Sept freeze. Account for 'release2' downloads dir.
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.100 lines changed: 1, context: html, text, full: html, text
    added new aplCal1 to list
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.92 lines changed: 12, context: html, text, full: html, text
    uldated cosmic data
• src/hg/makeDb/schema/all.joiner
  • 1.740 lines changed: 1, context: html, text, full: html, text
    Added pgSjk to tablesIgnored (thx Brooke).
  • 1.739 lines changed: 1, context: html, text, full: html, text
    suggested by qa
  • 1.738 lines changed: 1, context: html, text, full: html, text
    Adding hg19 to set of most recent 'knownGene' format databases.
  • 1.737 lines changed: 2, context: html, text, full: html, text
    adding danRer6
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.37 lines changed: 16, context: html, text, full: html, text
    adjusted priorities and set chainnets for equCab1 to o_db
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.59 lines changed: 5, context: html, text, full: html, text
    set shortLabel on hg18 chainnet tracks to o_db and set priority of chainNetHg19
• src/hg/makeDb/trackDb/horse/priority.ra
  • 1.2 lines changed: 5, context: html, text, full: html, text
    moved chainnets for canFam2 from priority.ra to trackDb.ra (override)
• src/hg/makeDb/trackDb/horse/trackDb.ra
  • 1.6 lines changed: 10, context: html, text, full: html, text
    added chain info for dog chain and adjusted priority for mousr chainnets
  • 1.5 lines changed: 8, context: html, text, full: html, text
    adjusted priority for human and dog chainnets
  • 1.4 lines changed: 13, context: html, text, full: html, text
    moved chainnets for canFam2 from priority.ra to trackDb.ra (override)
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Updated link -- annoying when a working link disappears.
• src/hg/makeDb/trackDb/human/hg18/trackDb.instinct.ra
  • 1.44 lines changed: 14, context: html, text, full: html, text
    New cosmic update
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.576 lines changed: 423, context: html, text, full: html, text
    Added 14 more Uw ChIP submissions
  • 1.575 lines changed: 166, context: html, text, full: html, text
    Added wgEncodeUwDgf tracks
  • 1.574 lines changed: 1561, context: html, text, full: html, text
    removed release beta blocks and release alpha lines from Yale TFBS tracks
  • 1.573 lines changed: 64, context: html, text, full: html, text
    Left out 2 Duke submissions
  • 1.572 lines changed: 1473, context: html, text, full: html, text
    More Duke tracks (added by Tracy) and reordered UW tracks
  • 1.571 lines changed: 32, context: html, text, full: html, text
    Fixed 'singals' typo in Yale metadata
  • 1.570 lines changed: 48, context: html, text, full: html, text
    use colors in bed rather than cell type color
  • 1.569 lines changed: 7, context: html, text, full: html, text
    A few more Yale metadata correctioons
  • 1.568 lines changed: 13, context: html, text, full: html, text
    defaults for the CSHL short rna track
  • 1.567 lines changed: 43, context: html, text, full: html, text
    Updating Yale metadata V2
  • 1.566 lines changed: 265, context: html, text, full: html, text
    CSHL short rna-seq: take out log signals, edit short labels, add sorting prefixes
  • 1.565 lines changed: 200, context: html, text, full: html, text
    Added 5 to Yale TFSB
  • 1.564 lines changed: 136, context: html, text, full: html, text
    Removed H3K4me1 from UwChIP and renamed BJ-tert to BJ by Stam lab request.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
  • 1.43 lines changed: 1, context: html, text, full: html, text
    release notes
  • 1.42 lines changed: 23, context: html, text, full: html, text
    a few tweaks to the new Notes section for this second release of the data
  • 1.41 lines changed: 1, context: html, text, full: html, text
    Added that olderversions of 'versioned' files are availabel through ftp
  • 1.40 lines changed: 9, context: html, text, full: html, text
    Third time is not yet charmed
  • 1.39 lines changed: 37, context: html, text, full: html, text
    Once is never enough. More cleanup to Notes
  • 1.38 lines changed: 60, context: html, text, full: html, text
    Added notes to Yale desc page
• src/hg/makeDb/trackDb/lizard/priority.ra
  • 1.2 lines changed: 6, context: html, text, full: html, text
    moved priority.ra into trackDb.ra, adjusted priority on chainNetHg19 and set shortLabel on hg18 chainnet tracks to o_db
• src/hg/makeDb/trackDb/lizard/trackDb.ra
  • 1.4 lines changed: 15, context: html, text, full: html, text
    moved priority.ra into trackDb.ra, adjusted priority on chainNetHg19 and set shortLabel on hg18 chainnet tracks to o_db
• src/hg/makeDb/trackDb/lowelab/description-template.html
  • 1.14 lines changed: 2, context: html, text, full: html, text
    add annotRev list to description page
• src/hg/makeDb/trackDb/lowelab/halMar1/trackDb.ra
  • 1.18 lines changed: 22, context: html, text, full: html, text
    comment out chainHalMar1 and blastzHalMar1
• src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra
  • 1.22 lines changed: 23, context: html, text, full: html, text
    comment out chainHalMar1 and blastzHalMar1
• src/hg/makeDb/trackDb/lowelab/haloVolc1_1/trackDb.ra
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Update annotRev track
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Update annotRev track
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Update annotRev track
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Update annotRev track
• src/hg/makeDb/trackDb/lowelab/peloCarb/trackDb.ra
  • 1.4 lines changed: 17, context: html, text, full: html, text
    delete old multiz track
• src/hg/makeDb/trackDb/lowelab/peloProp_DSM2379/trackDb.ra
  • 1.4 lines changed: 17, context: html, text, full: html, text
    delete old multiz track
• src/hg/makeDb/trackDb/lowelab/pyrAer1/description.html
  • 1.12 lines changed: 85, context: html, text, full: html, text
    fixed typo
• src/hg/makeDb/trackDb/medaka/priority.ra
  • 1.3 lines changed: 6, context: html, text, full: html, text
    set shortLabel on hg18 chainnet tracks to o_db, set priority of chainNetHg19 and some fish and moved some items from priority.ra
• src/hg/makeDb/trackDb/medaka/trackDb.ra
  • 1.15 lines changed: 21, context: html, text, full: html, text
    set shortLabel on hg18 chainnet tracks to o_db, set priority of chainNetHg19 and some fish and moved some items from priority.ra
• src/hg/makeDb/trackDb/mouse/igtc.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to EGTC.
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.20 lines changed: 10, context: html, text, full: html, text
    added dog chain and net override (because the chainNetCanFam2 at the top level is release alpha)
• src/hg/makeDb/trackDb/platypus/trackDb.ra
  • 1.4 lines changed: 13, context: html, text, full: html, text
    changed hg18 chainnets to o_db and set priorities of hg18 and hg19 chainnets
• src/hg/makeDb/trackDb/seaHare/aplCal1/description.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    adding link to Broad sequencing
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
  • 1.39 lines changed: 4, context: html, text, full: html, text
    set shortLabel on hg18 chainnet tracks to o_db
• src/hg/utils/automation/HgDb.pm
  • 1.7 lines changed: 25, context: html, text, full: html, text
    add disconnect, getChromSizes and DESTROY methods
• src/hg/utils/makefile
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Added refreshNamedSessionCustomTracks to DIRS.
• src/hg/visiGene/vgProbeTrack/vgProbeTrack.c
  • 1.14 lines changed: 3, context: html, text, full: html, text
    fix misleading name
  • 1.13 lines changed: 2, context: html, text, full: html, text
    yay, hgLoadChrom takes db arg now
• src/inc/common.mk
  • 1.71 lines changed: 1, context: html, text, full: html, text
    Use of samtools is spreading in the tree, so (if USE_BAM) add SAMLIB to L at the top level (inc/common.mk).
• src/inc/genoFind.h
  • 1.81 lines changed: 4, context: html, text, full: html, text
    Moving repMatch calculations from blat to library so can be shared with gfServer.
• src/jkOwnLib/genoFind.c
  • 1.26 lines changed: 48, context: html, text, full: html, text
    Moving repMatch calculations from blat to library so can be shared with gfServer.
• src/makefile
  • 1.65 lines changed: 5, context: html, text, full: html, text
    adding missing utils
• src/test/perllib/HgConf.pm
  • 1.3 lines changed: 38, context: html, text, full: html, text
    Support inclusion of other hg.conf files.
• src/utils/qa/findKgTableSet.csh
  • 1.1 lines changed: 64, context: html, text, full: html, text
    checked in script to get list of KG tables for current assembly from master list
• src/utils/qa/gsTables
  • 1.1 lines changed: 97, context: html, text, full: html, text
    added table lists for knownGene.csh script to use and removed some names from existing kgTables list
• src/utils/qa/kgTables
  • 1.3 lines changed: 20, context: html, text, full: html, text
    added table lists for knownGene.csh script to use and removed some names from existing kgTables list
• src/utils/qa/knownGene.csh
  • 1.13 lines changed: 71, context: html, text, full: html, text
    updated to work with new KG. still needs work
• src/utils/qa/makefile
  • 1.116 lines changed: 1, context: html, text, full: html, text
    checked in script to get list of KG tables for current assembly from master list
  • 1.115 lines changed: 2, context: html, text, full: html, text
    added table lists for knownGene.csh script to use and removed some names from existing kgTables list
• src/utils/qa/pbTables
  • 1.1 lines changed: 14, context: html, text, full: html, text
    added table lists for knownGene.csh script to use and removed some names from existing kgTables list
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.83 lines changed: 3, context: html, text, full: html, text
    v217 final build
• src/utils/qa/weeklybld/makeUserApps.csh
  • 1.7 lines changed: 1, context: html, text, full: html, text
    redirect output because 32bit utils build on titan for some reason leaks into the calling terminal output, but not on hgwbeta 64bit for some reason
• src/utils/userApps/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    since all other dates are changing, this one should too
  • 1.4 lines changed: 1, context: html, text, full: html, text
    qa does not want this doc file anymore on hgdownload

• lines changed: 7824
• files changed: 103