CVS changes by file

review to branch (2009-12-09 to 2009-12-14) v221

• src/hg/encode/encodeValidate/config/cv.ra
  • 1.155 lines changed: 1, context: html, text, full: html, text
    Greg Crawford finds his typo
  • 1.154 lines changed: 23, context: html, text, full: html, text
    Added one more cell line and updated others for Crawford. Fixed INFa4h concentration to what Greg specifically requested.
  • 1.153 lines changed: 115, context: html, text, full: html, text
    Added cell lines and treatments for Crawford. Will need to extend cell line definitions.
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • 1.95 lines changed: 1, context: html, text, full: html, text
    fix typo
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.510 lines changed: 5, context: html, text, full: html, text
    A couple other places where cds-reference needs to be omitted from the list of SNP functions if version >= 130 (Thanks again Katrina!). Also removed an extraneous comment left over from a branch tag move demo (1.429).
• src/hg/hgTracks/bamTrack.c
  • 1.19 lines changed: 13, context: html, text, full: html, text
    Got rid of bogus bamIgnoreStrand() -- make useStrand explicit. Added auto-detect of missing 'chr' in sequence names, so stripPrefix setting is no longer necessary. Better message for samopen failures.
• src/hg/hgTracks/hgTracks.c
  • 1.1614 lines changed: 6, context: html, text, full: html, text
    Okay, really fix it.
  • 1.1613 lines changed: 2, context: html, text, full: html, text
    Fixed bug in centerLabel toggle seen on mrna track when withNextItemArrows is FALSE
• src/hg/hgc/bamClick.c
  • 1.13 lines changed: 24, context: html, text, full: html, text
    Got rid of bogus bamIgnoreStrand() -- make useStrand explicit. Added auto-detect of missing 'chr' in sequence names, so stripPrefix setting is no longer necessary. Better message for samopen failures.
• src/hg/hgc/hgc.c
  • 1.1583 lines changed: 69, context: html, text, full: html, text
    Added logic to handle non-dbSnp entries of 3 new Illumina SNP arrays.
• src/hg/inc/bamFile.h
  • 1.13 lines changed: 16, context: html, text, full: html, text
    Got rid of bogus bamIgnoreStrand() -- make useStrand explicit. Added auto-detect of missing 'chr' in sequence names, so stripPrefix setting is no longer necessary. Better message for samopen failures.
• src/hg/inc/hui.h
  • 1.144 lines changed: 4, context: html, text, full: html, text
    'Color by bases' labels: use 'mRNA bases' only when we have coding region info; otherwise, use 'item bases' because items are generally not mRNAs.
• src/hg/inc/versionInfo.h
  • 1.162 lines changed: 1, context: html, text, full: html, text
    "New version number v221"
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_kotliarov2006.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    
• src/hg/js/hui.js
  • 1.46 lines changed: 2, context: html, text, full: html, text
    Really fixed.
  • 1.45 lines changed: 2, context: html, text, full: html, text
    Fixed bug in propgating view level radio button cfg to the subtracks
• src/hg/lib/bamFile.c
  • 1.17 lines changed: 52, context: html, text, full: html, text
    Got rid of bogus bamIgnoreStrand() -- make useStrand explicit. Added auto-detect of missing 'chr' in sequence names, so stripPrefix setting is no longer necessary. Better message for samopen failures.
• src/hg/lib/customFactory.c
  • 1.113 lines changed: 3, context: html, text, full: html, text
    unlink the custom wia file after it is open so it will disappear if the loader fails
• src/hg/lib/customTrack.c
  • 1.180 lines changed: 1, context: html, text, full: html, text
    Null check to prevent segv in command line runs (cgiScriptName returns NULL unless env var SCRIPT_NAME has been set).
• src/hg/lib/hui.c
  • 1.252 lines changed: 4, context: html, text, full: html, text
    'Color by bases' labels: use 'mRNA bases' only when we have coding region info; otherwise, use 'item bases' because items are generally not mRNAs.
• src/hg/lib/wiggleCart.c
  • 1.36 lines changed: 7, context: html, text, full: html, text
    backward autoScale default for custom tracks, have autoScale on by default
• src/hg/makeDb/doc/galGal3.txt
  • 1.33 lines changed: 1, context: html, text, full: html, text
    finished condor 454 item base coloring
• src/hg/makeDb/doc/hg18.txt
  • 1.391 lines changed: 62, context: html, text, full: html, text
    Added documentation for making track of Burge lab RNA-seq reads mapped by GEM mapper.
• src/hg/makeDb/doc/hg19.txt
  • 1.67 lines changed: 66, context: html, text, full: html, text
    Added documentation for making track of Burge lab RNA-seq reads mapped by GEM mapper.
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.101 lines changed: 1, context: html, text, full: html, text
    turning on danRer6
• src/hg/makeDb/schema/all.joiner
  • 1.753 lines changed: 2, context: html, text, full: html, text
    mm9 is now based on hg19 for TransMap
  • 1.752 lines changed: 2, context: html, text, full: html, text
    cleaning up transMapGeneUcscGenesId (approved by markd)
  • 1.751 lines changed: 2, context: html, text, full: html, text
    adding hg19 to CGAP rule
  • 1.750 lines changed: 1, context: html, text, full: html, text
    added the last two sp databases to databasesIgnored list
  • 1.749 lines changed: 11, context: html, text, full: html, text
    two new SCOP rules
  • 1.748 lines changed: 5, context: html, text, full: html, text
    new rule for pfam relationship
  • 1.747 lines changed: 1, context: html, text, full: html, text
    loosened up allenbrain rule
  • 1.746 lines changed: 5, context: html, text, full: html, text
    added a missing rule for TransMap tables
  • 1.745 lines changed: 2, context: html, text, full: html, text
    oops. joining lines.
  • 1.744 lines changed: 3, context: html, text, full: html, text
    correcting list of dbs for which transMap is built
• src/hg/makeDb/trackDb/README
  • 1.95 lines changed: 9, context: html, text, full: html, text
    Indicate the loading procedure for a bigWig file.
• src/hg/makeDb/trackDb/alpaca/vicPac1/trackDb.ra
  • 1.2 lines changed: 19, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/ancestor/borEut13/trackDb.ra
  • 1.9 lines changed: 82, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/ancestor/canHg10/trackDb.ra
  • 1.10 lines changed: 78, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/ancestor/canHg11/trackDb.ra
  • 1.5 lines changed: 78, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/canHg12/trackDb.ra
  • 1.7 lines changed: 82, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/canHg4/trackDb.ra
  • 1.12 lines changed: 67, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/canHg9/trackDb.ra
  • 1.7 lines changed: 65, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/car46/trackDb.ra
  • 1.9 lines changed: 65, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/catArr1/trackDb.ra
  • 1.6 lines changed: 82, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/euaGli13/trackDb.ra
  • 1.5 lines changed: 82, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/gliRes13/trackDb.ra
  • 1.5 lines changed: 82, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/homIni13/trackDb.ra
  • 1.8 lines changed: 65, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/homIni14/trackDb.ra
  • 1.7 lines changed: 74, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/homIni20/trackDb.ra
  • 1.5 lines changed: 20, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/homPan20/trackDb.ra
  • 1.5 lines changed: 21, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/priMat13/trackDb.ra
  • 1.7 lines changed: 82, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/rodEnt13/trackDb.ra
  • 1.5 lines changed: 82, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/ancestor/trackDb.ra
  • 1.9 lines changed: 28, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/anopheles/trackDb.ra
  • 1.19 lines changed: 48, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/apis/apiMel1/trackDb.ra
  • 1.11 lines changed: 9, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/apis/apiMel2/trackDb.ra
  • 1.26 lines changed: 27, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/apis/trackDb.ra
  • 1.14 lines changed: 29, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/armadillo/dasNov2/trackDb.ra
  • 1.2 lines changed: 19, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra
  • 1.2 lines changed: 19, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/cat/felCat3/trackDb.ra
  • 1.24 lines changed: 35, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/cat/trackDb.ra
  • 1.6 lines changed: 4, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/chainBosTau2.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    fixup chainNet priorities for bosTau2
• src/hg/makeDb/trackDb/chicken/galGal1/trackDb.ra
  • 1.15 lines changed: 31, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/chicken/galGal2/trackDb.ra
  • 1.72 lines changed: 115, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/chicken/galGal3/trackDb.ra
  • 1.16 lines changed: 2, context: html, text, full: html, text
    finished condor 454 item base coloring
  • 1.15 lines changed: 4, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/chicken/trackDb.ra
  • 1.16 lines changed: 2, context: html, text, full: html, text
    A few fixes from release tag being lost in child during override.
  • 1.15 lines changed: 44, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra
  • 1.39 lines changed: 44, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.46 lines changed: 102, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • 1.24 lines changed: 71, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/cow/bosTau1/trackDb.ra
  • 1.18 lines changed: 47, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/cow/bosTau2/trackDb.ra
  • 1.9 lines changed: 38, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/cow/bosTau3/trackDb.ra
  • 1.8 lines changed: 20, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.19 lines changed: 19, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/cow/trackDb.ra
  • 1.5 lines changed: 58, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/dog/canFam1/trackDb.ra
  • 1.37 lines changed: 53, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.40 lines changed: 13, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/dog/canFamPoodle1/trackDb.ra
  • 1.2 lines changed: 19, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    felCat3 chain and nets are now composites
  • 1.1 lines changed: 4, context: html, text, full: html, text
    bosTau4 chain and net is now ready for composite
• src/hg/makeDb/trackDb/dog/trackDb.ra
  • 1.27 lines changed: 93, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/dolphin/turTru1/trackDb.ra
  • 1.2 lines changed: 19, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/drosophila/dm1/trackDb.ra
  • 1.60 lines changed: 30, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra
  • 1.59 lines changed: 139, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra
  • 1.15 lines changed: 19, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/dp1/trackDb.ra
  • 1.15 lines changed: 14, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/dp2/trackDb.ra
  • 1.12 lines changed: 21, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/dp3/trackDb.ra
  • 1.16 lines changed: 74, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/droAna1/trackDb.ra
  • 1.14 lines changed: 68, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/droAna2/trackDb.ra
  • 1.12 lines changed: 17, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/droEre1/trackDb.ra
  • 1.13 lines changed: 46, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/droGri1/trackDb.ra
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• src/hg/makeDb/trackDb/drosophila/droMoj1/trackDb.ra
  • 1.13 lines changed: 67, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/droMoj2/trackDb.ra
  • 1.6 lines changed: 46, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/droPer1/trackDb.ra
  • 1.4 lines changed: 33, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/droSec1/trackDb.ra
  • 1.3 lines changed: 33, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/droSim1/trackDb.ra
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• src/hg/makeDb/trackDb/drosophila/droVir1/trackDb.ra
  • 1.13 lines changed: 67, context: html, text, full: html, text
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• src/hg/makeDb/trackDb/drosophila/droVir2/trackDb.ra
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• src/hg/makeDb/trackDb/drosophila/droYak1/trackDb.ra
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• src/hg/makeDb/trackDb/drosophila/droYak2/trackDb.ra
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• src/hg/makeDb/trackDb/drosophila/trackDb.ra
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• src/hg/makeDb/trackDb/elephant/loxAfr2/trackDb.ra
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• src/hg/makeDb/trackDb/elephant/loxAfr3/trackDb.ra
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• src/hg/makeDb/trackDb/fugu/fr1/trackDb.ra
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• src/hg/makeDb/trackDb/fugu/fr2/trackDb.ra
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• src/hg/makeDb/trackDb/fugu/trackDb.ra
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• src/hg/makeDb/trackDb/gorilla/gorGor1/trackDb.ra
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• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra
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• src/hg/makeDb/trackDb/haplotypes/hg19Haps/trackDb.ra
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• src/hg/makeDb/trackDb/hedgehog/eriEur1/trackDb.ra
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• src/hg/makeDb/trackDb/hiv/hiv1/trackDb.ra
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• src/hg/makeDb/trackDb/hiv/hivVax003Vax004/trackDb.ra
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• src/hg/makeDb/trackDb/hiv/hiva244/trackDb.ra
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• src/hg/makeDb/trackDb/hiv/hivgne8/trackDb.ra
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• src/hg/makeDb/trackDb/hiv/hivgne8v2/trackDb.ra
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• src/hg/makeDb/trackDb/hiv/hivmn/trackDb.ra
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• src/hg/makeDb/trackDb/hiv/hivmn1/trackDb.ra
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• src/hg/makeDb/trackDb/hiv/hivmn2/trackDb.ra
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• src/hg/makeDb/trackDb/horse/equCab1/trackDb.ra
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• src/hg/makeDb/trackDb/horse/equCab2/trackDb.ra
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• src/hg/makeDb/trackDb/horse/trackDb.ra
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• src/hg/makeDb/trackDb/human/hg12/trackDb.ra
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• src/hg/makeDb/trackDb/human/hg13/trackDb.ra
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• src/hg/makeDb/trackDb/human/hg15/trackDb.ra
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• src/hg/makeDb/trackDb/human/hg16/trackDb.encode.ra
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• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
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• src/hg/makeDb/trackDb/human/hg17/bosTau2.chainNet.html
  • 1.2 lines changed: 153, context: html, text, full: html, text
    no need to have bosTau2.chainNet here
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
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• src/hg/makeDb/trackDb/human/hg18/burgeRnaSeqGemMapperAlign.html
  • 1.2 lines changed: 7, context: html, text, full: html, text
    Editing of description.
• src/hg/makeDb/trackDb/human/hg18/snpArray.html
  • 1.16 lines changed: 53, context: html, text, full: html, text
    Updated SNP Arrays description page for new Illumina products and remove their old ones.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChip.ra
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• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChrom.ra
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• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeCompAndVar.ra
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• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeGenes.ra
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• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.440 lines changed: 107, context: html, text, full: html, text
    Removed Burge RNA-seq data entry and added it to human trackDb level since the settings are the same for hg18 and hg19.
  • 1.439 lines changed: 27, context: html, text, full: html, text
    Added search terms for 3 new Illumina SNP array chips.
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    Put back snpArrayIllumina650.
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfIsla_L_S_2_15/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_14_25/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_16_27/trackDb.ra
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_16_4/trackDb.ra
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfIsla_ROD_SHAPED_V/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfIsla_ROD_SHAPED_VIRUS_2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfIsla_Y_G_57_14/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfIsla_Y_N_15_51/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfSpin_VIRUS_4/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfToko1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfTurr_ICOSAHEDRAL/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfViru_1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfViru_2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfViru_KAMCHATKA_1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfViru_RAGGED_HILLS/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/sulfViru_STSV1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/syneElon_PCC_7942/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/testPae/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/testTne/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therAcid1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therBaro0/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therGamm1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therKoda1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therNeut0/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therNeut1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therOnnu1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therPend1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therSibi1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therTena1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therTena_SPHERICAL_VI/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/therVolc1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/uncuMeth_RCI/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/vibrChol1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/vibrFisc_ES114_1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/vibrPara1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/vibrVuln_CMCP6_1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/vibrVuln_YJ016_1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/vulcDist0/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/xantAuto_PY2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/yersPseu_IP31758/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/lowelab/yersPseu_IP32953/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/marmoset/calJac1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/marmoset/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/medaka/oryLat1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/medaka/oryLat2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/medaka/trackDb.ra
  • 1.19 lines changed: 39, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/microbat/myoLuc1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouse/chainBosTau2.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fixup chainNet priorities for bosTau2
• src/hg/makeDb/trackDb/mouse/mm2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouse/mm2X/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouse/mm3/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouse/mm3X/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouse/mm4/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouse/mm5/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouse/mm6/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouse/mm7/bosTau2.chainNet.html
  • 1.2 lines changed: 153, context: html, text, full: html, text
    no need to have bosTau2.chainNet here
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • 1.4 lines changed: 3, context: html, text, full: html, text
    felCat3 chain and nets are now composites
  • 1.3 lines changed: 5, context: html, text, full: html, text
    bosTau4 chain and net is now ready for composite
  • 1.2 lines changed: 7, context: html, text, full: html, text
    bosTau3 is now ready for chainNet composite
  • 1.1 lines changed: 5, context: html, text, full: html, text
    fixup chainNet priorities for bosTau2
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.167 lines changed: 2, context: html, text, full: html, text
    bosTau3 is now ready for chainNet composite
  • 1.166 lines changed: 1, context: html, text, full: html, text
    add chainMinScore to the bosTau2 chain entries
  • 1.165 lines changed: 5, context: html, text, full: html, text
    fixup chainNet priorities for bosTau2
  • 1.164 lines changed: 278, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/opossum/monDom1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/opossum/monDom2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/opossum/monDom4/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/opossum/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/orangutan/ponAbe1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/orangutan/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/other/nemVec1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/pika/ochPri2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/platypus/ornAna1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
  • 1.1 lines changed: 6, context: html, text, full: html, text
    bosTau4 chain and net is now ready for composite
• src/hg/makeDb/trackDb/platypus/trackDb.ra
  • 1.9 lines changed: 13, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/rat/rn1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/rat/rn2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/rat/rn3/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/rat/rn5/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    bosTau4 chain and net is now ready for composite
  • 1.1 lines changed: 5, context: html, text, full: html, text
    bosTau3 is now ready for chainNet composite
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • 1.61 lines changed: 1, context: html, text, full: html, text
    A few fixes from release tag being lost in child during override.
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/rhesus/rheMac1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/rockHyrax/proCap1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/rockHyrax/proCav1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/sars/sc1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/seaHare/aplCal1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/shrew/sorAra1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/sloth/choHof1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/squirrel/speTri1/trackDb.ra
  • 1.2 lines changed: 19, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/squirt/ci1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/squirt/ci2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/squirt/cioSav1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/squirt/cioSav2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/squirt/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/stickleback/gasAcu1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/stickleback/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/tarsier/tarSyr1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/tenrec/echTel1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/tetraodon/tetNig1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.7 lines changed: 58, context: html, text, full: html, text
    felCat3 chain and nets are now composites
  • 1.6 lines changed: 42, context: html, text, full: html, text
    bosTau4 chain and net is now ready for composite
  • 1.5 lines changed: 43, context: html, text, full: html, text
    bosTau3 is now ready for chainNet composite
  • 1.4 lines changed: 42, context: html, text, full: html, text
    fixup chainNet priorities for bosTau2
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.554 lines changed: 6, context: html, text, full: html, text
    felCat3 chain and nets are now composites
  • 1.553 lines changed: 5, context: html, text, full: html, text
    bosTau4 chain and net is now ready for composite
  • 1.552 lines changed: 5, context: html, text, full: html, text
    bosTau3 is now ready for chainNet composite
  • 1.551 lines changed: 1, context: html, text, full: html, text
    add chainMinScore to the bosTau2 chain entries
  • 1.550 lines changed: 32, context: html, text, full: html, text
    fixup chainNet priorities for bosTau2
• src/hg/makeDb/trackDb/urchin/strPur1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/urchin/strPur2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/venter/venter1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/caeJap1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/caeJap2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/caePb1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/caePb2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/caeRem2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/caeRem3/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/cb1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/cb3/trackDb.ra
  • 1.6 lines changed: 59, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/ce1/trackDb.ra
  • 1.40 lines changed: 28, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/ce2/trackDb.ra
  • 1.37 lines changed: 31, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/ce3/trackDb.ra
  • 1.10 lines changed: 6, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/ce4/trackDb.ra
  • 1.40 lines changed: 86, context: html, text, full: html, text
    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/ce5/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/ce6/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/ce7/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/ce8/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/priPac1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/worm/trackDb.ra
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    Needed some release alpha tags to avoid errors
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/xenTro/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/zebraFinch/taeGut1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/zebraFinch/trackDb.ra
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    A few fixes from release tag being lost in child during override.
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/zebrafish/danRer1/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/zebrafish/danRer2/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra
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    third time's the charm. needed to set to pack. default was dense
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    reset so xenoRefGene is visible. more interesting at new defulat pos
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    set human chain to pack and xenoRefGene to hide as default
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    Run of tdbRewriteReduceReplaces.
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
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    Run of tdbRewriteReduceReplaces.
• src/hg/oneShot/tdbRewriteViewsToSubtracks/tdbRewriteViewsToSubtracks.c
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    Tightening up identification of composite tracks with views. Adding in some things from branch.
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    Adding view tag to view.
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    Adding shortLabel to view. Fixing small indentation problem.
• src/hg/qaPushQ/qaPushQ.c
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    adding closing tag
• src/hg/utils/phyloTrees/chainNet.pl
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    Eliminate much of the garbage from other chain tables and find appropriate tree in the phylo tree
• src/hg/utils/phyloTrees/findScores.pl
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    Check chain.csh file in lastz/blastz run for parameters
• src/hg/utils/tdbQuery/tdbQuery.c
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    Improving error message.
• src/inc/cheapcgi.h
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    no trailing asterix needed
• src/lib/cheapcgi.c
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    no trailing asterix needed
• src/product/ex.hg.conf
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    No need to mention the cookie
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    Fixup central.domain and central.cookie comments
• src/utils/qa/alertBqueue.csh
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    fixed so it will not complain about staged encode tracks in B-queue that have no reviewer and have not been in A-queue
• src/utils/qa/weeklybld/buildEnv.csh
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    v221 final build

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• files changed: 397