CVS changes by file

branch to review (2009-09-15 to 2009-09-22) v216

• src/hg/archaeStuff/data/Genome-info-meta
  • 1.10 lines changed: 3, context: html, text, full: html, text
    add cold cren to BED alignments
  • 1.9 lines changed: 204, context: html, text, full: html, text
    add site 3, 4, 8, 14, 19, and BED
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.80 lines changed: 4, context: html, text, full: html, text
    align ospSpri14_050609_1 with hydrogenobaculum
  • 1.79 lines changed: 4, context: html, text, full: html, text
    adding utahensis
• src/hg/archaeStuff/data/blat-servers.tab
  • 1.4 lines changed: 1, context: html, text, full: html, text
    add Metagenome to lowepub
  • 1.3 lines changed: 2, context: html, text, full: html, text
    put blat server of Gammaproteobacteria onto lowedev
• src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm
  • 1.23 lines changed: 1, context: html, text, full: html, text
    set max displayed hits of blastx
  • 1.22 lines changed: 0, context: html, text, full: html, text
    add Andrew's gene prediction tracks; minor bug fixes; add common bin dir to Constants.pm; add gene finder prefix to predicted gene names
  • 1.21 lines changed: 3, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.35 lines changed: 11, context: html, text, full: html, text
    add Andrew's gene prediction tracks; minor bug fixes; add common bin dir to Constants.pm; add gene finder prefix to predicted gene names
• src/hg/archaeStuff/scripts/archaeBrowser/GenePrediction.pm
  • 1.8 lines changed: 72, context: html, text, full: html, text
    add Andrew's gene prediction tracks; minor bug fixes; add common bin dir to Constants.pm; add gene finder prefix to predicted gene names
• src/hg/archaeStuff/scripts/archaeBrowser/GenomeInfo.pm
  • 1.15 lines changed: 15, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/MultiAlignment.pm
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Changed default trackDb.ra setting for ultraConserved track from pack to dense.
• src/hg/archaeStuff/scripts/archaeBrowser/Organism.pm
  • 1.9 lines changed: 8, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.41 lines changed: 90, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/Utils.pm
  • 1.3 lines changed: 15, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm
  • 1.19 lines changed: 155, context: html, text, full: html, text
    add rRNA_Blat track
  • 1.18 lines changed: 1, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.47 lines changed: 4, context: html, text, full: html, text
    add rRNA_Blat track
  • 1.46 lines changed: 15, context: html, text, full: html, text
    add Andrew's gene prediction tracks; minor bug fixes; add common bin dir to Constants.pm; add gene finder prefix to predicted gene names
• src/hg/encode/DAFs/UwChIPseq.daf
  • 1.1 lines changed: 50, context: html, text, full: html, text
    New order of the day. DAFs must have dafVersion 1.1
• src/hg/encode/DAFs/UwDnaseSeq.daf
  • 1.7 lines changed: 9, context: html, text, full: html, text
    view RawSignal
• src/hg/encode/DAFs/YDHChipSeq.daf
  • 1.1 lines changed: 39, context: html, text, full: html, text
    New order of the day. DAFs must have dafVersion 1.1
• src/hg/encode/DAFs/YDHChipSeqInput.daf
  • 1.1 lines changed: 33, context: html, text, full: html, text
    New order of the day. DAFs must have dafVersion 1.1
• src/hg/encode/DAFs/YDHChipSeqTreatment.daf
  • 1.1 lines changed: 39, context: html, text, full: html, text
    New order of the day. DAFs must have dafVersion 1.1
• src/hg/encode/DAFs/YDHRnaSeq.daf
  • 1.1 lines changed: 33, context: html, text, full: html, text
    New order of the day. DAFs must have dafVersion 1.1
• src/hg/encode/DAFs/YDHRnaSeqTreatment.daf
  • 1.1 lines changed: 35, context: html, text, full: html, text
    New order of the day. DAFs must have dafVersion 1.1
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.128 lines changed: 3, context: html, text, full: html, text
    Changed antibody TCF4 to TC7L2
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.194 lines changed: 3, context: html, text, full: html, text
    Fix a bug when no 'validationSettings' are provided.
• src/hg/gsid/gsidTable/gsidTable.c
  • 1.47 lines changed: 31, context: html, text, full: html, text
    Added missing item processing logic for text output.
  • 1.46 lines changed: 4, context: html, text, full: html, text
    Added logic to check NULL for string cols.
  • 1.45 lines changed: 9, context: html, text, full: html, text
    Checked in a fix and additional logic to process "N/A".
• src/hg/gsid/gsidTable/gsidTableData/columnDb.ra
  • 1.22 lines changed: 7, context: html, text, full: html, text
    Turn off all new cols except "ART Sequencing".
  • 1.21 lines changed: 1, context: html, text, full: html, text
    Changed "ESDI Basis" to string intead of integer.
  • 1.20 lines changed: 89, context: html, text, full: html, text
    Checked in ART related new fileds.
• src/hg/hgTracks/hgTracks.c
  • 1.1599 lines changed: 6, context: html, text, full: html, text
    Special link for hg18 ncbi build36
  • 1.1598 lines changed: 7, context: html, text, full: html, text
    Proper NCBI blue bar links for hg18 and hg19
• src/hg/hgTracks/simpleTracks.c
  • 1.104 lines changed: 5, context: html, text, full: html, text
    Changed REST to rest.
  • 1.103 lines changed: 2, context: html, text, full: html, text
    Updated color logic for REST per Andy's suggestion.
• src/hg/hgTracks/wigTrack.c
  • 1.93 lines changed: 1, context: html, text, full: html, text
    allow alwaysZero to be set in trackDb, set to off by default
• src/hg/hgc/hgc.c
  • 1.1572 lines changed: 4, context: html, text, full: html, text
    fix memory trashing bug that's been here for ages. Thanks Brooke!
• src/hg/hgc/lowelab.c
  • 1.35 lines changed: 2, context: html, text, full: html, text
    check existence of scaffolds table for metagenome blastx track
• src/hg/inc/hui.h
  • 1.138 lines changed: 2, context: html, text, full: html, text
    allow alwaysZero to be set in trackDb, set to off by default
• src/hg/instinct/bioInt2/bioPathwayLevel.c
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Updating to latest stuff
• src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c
  • 1.3 lines changed: 7, context: html, text, full: html, text
    Updating to latest stuff
• src/hg/instinct/bioInt2/factorGraph/addEvidenceDaiFG.py
  • 1.3 lines changed: 163, context: html, text, full: html, text
    Updating to latest stuff
• src/hg/instinct/bioInt2/factorGraph/pathwayPerturbation
  • 1.3 lines changed: 0, context: html, text, full: html, text
    Updating to latest stuff
• src/hg/instinct/bioInt2/factorGraph/pathwaytab2daifg.py
  • 1.3 lines changed: 251, context: html, text, full: html, text
    Updating to latest stuff
• src/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.72 lines changed: 4, context: html, text, full: html, text
    fixed off by one in stats
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_TARGET.ra
  • 1.1 lines changed: 153, context: html, text, full: html, text
    New dataset
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenOVBio.ra
  • 1.10 lines changed: 55, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_kotliarov2006.ra
  • 1.1 lines changed: 9, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.23 lines changed: 54, context: html, text, full: html, text
    New datasets
  • 1.22 lines changed: 29, context: html, text, full: html, text
    New dataset
• src/hg/js/hgTracks.js
  • 1.43 lines changed: 2, context: html, text, full: html, text
    One last change to make sure chromDrag off right end can still pick up selection
  • 1.42 lines changed: 44, context: html, text, full: html, text
    A bit more cleanup and make sure that after doing the chromDrag selection no more chromDrag code is called.
  • 1.41 lines changed: 159, context: html, text, full: html, text
    Fixed... scrolling, reverse, cyto-band coordinates and cleaned up.
• src/hg/lib/customFactory.c
  • 1.103 lines changed: 6, context: html, text, full: html, text
    Making sure that bigWig or bigBed file referred to in bigDataUrl actually exists.
• src/hg/lib/ensFace.c
  • 1.13 lines changed: 9, context: html, text, full: html, text
    Special Ensembl link for hg18 ncbi build36
• src/hg/lib/hui.c
  • 1.237 lines changed: 11, context: html, text, full: html, text
    allow alwaysZero to be set in trackDb, set to off by default
• src/hg/lib/liftOver.c
  • 1.47 lines changed: 4, context: html, text, full: html, text
    Properly free the second subChain
  • 1.46 lines changed: 23, context: html, text, full: html, text
    Fix up memory management in the remapRange loop
• src/hg/lib/wgRna.as
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Edited table name and order of RNA types.
  • 1.1 lines changed: 13, context: html, text, full: html, text
    Created description for the wgRna table for the sno/miRNA track.
• src/hg/lib/wiggleCart.c
  • 1.22 lines changed: 5, context: html, text, full: html, text
    allow alwaysZero to be set in trackDb, set to off by default
• src/hg/makeDb/doc/anoCar1.txt
  • 1.22 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/bosTau4.txt
  • 1.18 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/caeJap2.txt
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Turned on updates for genbank
• src/hg/makeDb/doc/calJac1.txt
  • 1.20 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/canFam2.txt
  • 1.25 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/cavPor3.txt
  • 1.20 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/danRer5.txt
  • 1.18 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/danRer6.txt
  • 1.8 lines changed: 19, context: html, text, full: html, text
    Completed tetNig2 chains and nets to everything
• src/hg/makeDb/doc/dasNov1.txt
  • 1.8 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/echTel1.txt
  • 1.7 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/equCab2.txt
  • 1.28 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/felCat3.txt
  • 1.55 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/fr2.txt
  • 1.25 lines changed: 9, context: html, text, full: html, text
    transmap build
  • 1.24 lines changed: 27, context: html, text, full: html, text
    Completed tetNig2 chains and nets to everything
• src/hg/makeDb/doc/galGal3.txt
  • 1.30 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/gasAcu1.txt
  • 1.38 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/hg17.txt
  • 1.123 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/hg18.txt
  • 1.383 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/hg19.txt
  • 1.38 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/loxAfr3.txt
  • 1.5 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/mm8.txt
  • 1.75 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/mm9.txt
  • 1.115 lines changed: 5, context: html, text, full: html, text
    Fixed the base 0 problem for REST track.
  • 1.114 lines changed: 9, context: html, text, full: html, text
    transmap build
  • 1.113 lines changed: 60, context: html, text, full: html, text
    Completed tetNig2 chains and nets to everything
  • 1.112 lines changed: 16, context: html, text, full: html, text
    Added REST track.
• src/hg/makeDb/doc/monDom4.txt
  • 1.17 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/monDom5.txt
  • 1.15 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/ornAna1.txt
  • 1.27 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/oryCun2.txt
  • 1.2 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/oryLat2.txt
  • 1.14 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/otoGar1.txt
  • 1.10 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/panTro2.txt
  • 1.17 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/petMar1.txt
  • 1.22 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/ponAbe2.txt
  • 1.22 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/rheMac2.txt
  • 1.18 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/rn4.txt
  • 1.34 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/taeGut1.txt
  • 1.19 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/tetNig1.txt
  • 1.20 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/doc/tetNig2.txt
  • 1.7 lines changed: 9, context: html, text, full: html, text
    transmap build
  • 1.6 lines changed: 196, context: html, text, full: html, text
    Completed tetNig2 chains and nets to everything
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh
  • 1.1 lines changed: 1194, context: html, text, full: html, text
    Far enough into rebuild should save the as ever slightly tweaked instructions.
• src/hg/makeDb/doc/xenTro2.txt
  • 1.15 lines changed: 9, context: html, text, full: html, text
    transmap build
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.100 lines changed: 1, context: html, text, full: html, text
    Added caeJap2 - C. japonica
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.105 lines changed: 1, context: html, text, full: html, text
    Added caeJap2 - C. japonica
• src/hg/makeDb/genbank/etc/ignore.idx
  • 1.95 lines changed: 1, context: html, text, full: html, text
    added ignore item
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.90 lines changed: 25, context: html, text, full: html, text
    New datasets
  • 1.89 lines changed: 10, context: html, text, full: html, text
    New dataset
• src/hg/makeDb/schema/all.joiner
  • 1.735 lines changed: 3, context: html, text, full: html, text
    added mm9.rest to tablesIgnored
• src/hg/makeDb/trackDb/cat/felCat3/trackDb.ra
  • 1.22 lines changed: 2, context: html, text, full: html, text
    restoring Human to longLabel on hg18 chain/net tracks
  • 1.21 lines changed: 20, context: html, text, full: html, text
    primate and mammal chain reordering, etc. reduced some influence of stay priority.ra files
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.44 lines changed: 17, context: html, text, full: html, text
    reordered chainnets (again - how do they keep getting messd up?) and set old monDom4s to o_db shortLabel
  • 1.43 lines changed: 2, context: html, text, full: html, text
    returned hg18 longLabel to Human
  • 1.42 lines changed: 2, context: html, text, full: html, text
    primate and mammal chain reordering, etc. reduced some influence of stay priority.ra files
  • 1.41 lines changed: 8, context: html, text, full: html, text
    moved override stuff to bottom of track blocks
  • 1.40 lines changed: 22, context: html, text, full: html, text
    moved override stuff to bottom of track blocks
• src/hg/makeDb/trackDb/chimp/priority.ra
  • 1.5 lines changed: 19, context: html, text, full: html, text
    combined priority.ra into trackDb.ra
• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • 1.23 lines changed: 18, context: html, text, full: html, text
    moved chimp priority.ra into trackDb.ra
  • 1.22 lines changed: 11, context: html, text, full: html, text
    moved override blocks together
  • 1.21 lines changed: 16, context: html, text, full: html, text
    converted dbChainNet trackNames to chainNetDb to match pattern we've been using
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.16 lines changed: 2, context: html, text, full: html, text
    restored org name to longLabel
  • 1.15 lines changed: 14, context: html, text, full: html, text
    primate and mammal chain reordering, etc. reduced some influence of stay priority.ra files
  • 1.14 lines changed: 6, context: html, text, full: html, text
    moved override stuff to bottom of track blocks
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.35 lines changed: 3, context: html, text, full: html, text
    restoring Human to longLabel on hg18 chain/net tracks
  • 1.34 lines changed: 42, context: html, text, full: html, text
    primate and mammal chain reordering, etc. reduced some influence of stay priority.ra files
  • 1.33 lines changed: 8, context: html, text, full: html, text
    moved override stuff to bottom of track blocks
• src/hg/makeDb/trackDb/dog/priority.ra
  • 1.7 lines changed: 27, context: html, text, full: html, text
    primate and mammal chain reordering, etc. reduced some influence of stay priority.ra files
• src/hg/makeDb/trackDb/dog/trackDb.ra
  • 1.23 lines changed: 29, context: html, text, full: html, text
    primate and mammal chain reordering, etc. reduced some influence of stay priority.ra files
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.58 lines changed: 18, context: html, text, full: html, text
    Updating chainNet composite tracks for tetNig2, fr2, oryLat2, danRer6, hg19, mm9
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra
  • 1.6 lines changed: 20, context: html, text, full: html, text
    primate and mammal chain reordering, etc. reduced some influence of stay priority.ra files
• src/hg/makeDb/trackDb/human/hg18/trackDb.instinct.ra
  • 1.43 lines changed: 25, context: html, text, full: html, text
    New datasets
  • 1.42 lines changed: 11, context: html, text, full: html, text
    hopefully fixed this by removing CVS conflict lines that were accidentally committed
  • 1.41 lines changed: 34, context: html, text, full: html, text
    New dataset
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.419 lines changed: 2, context: html, text, full: html, text
    returned monDom4 shortLabel back to Opossum, because not pushing monDom5 chainnet set after all
  • 1.418 lines changed: 2, context: html, text, full: html, text
    changed shortLabel for old monDom4 chainnets
• src/hg/makeDb/trackDb/human/hg18/trackDb.tcga1.ra
  • 1.22 lines changed: 3, context: html, text, full: html, text
    changed color scaling (expScale) for a few datasets
  • 1.21 lines changed: 36, context: html, text, full: html, text
    added maxItems 2000 to all entries
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.529 lines changed: 146, context: html, text, full: html, text
    add wiggles for CSHL long rna tagAligns
  • 1.528 lines changed: 26, context: html, text, full: html, text
    Changed antibody TCF4 to TCF7L2
  • 1.527 lines changed: 2, context: html, text, full: html, text
    Oops. YaleRnaSeq no longer has view, but left the subGroup
  • 1.526 lines changed: 23, context: html, text, full: html, text
    new CSHL long rnaSeq
  • 1.525 lines changed: 2469, context: html, text, full: html, text
    Removed a bunch of RawSignals from Broad and Yale
  • 1.524 lines changed: 84, context: html, text, full: html, text
    Post-release tweak to defaults: more logical view ordering, suppress rep2 by default
  • 1.523 lines changed: 168, context: html, text, full: html, text
    5C to regulation, CSHL long RNA tables
  • 1.522 lines changed: 117, context: html, text, full: html, text
    5C test track.
  • 1.521 lines changed: 1, context: html, text, full: html, text
    set visibility to hide for a track
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.50 lines changed: 10, context: html, text, full: html, text
    primate and mammal chain reordering, etc. reduced some influence of stay priority.ra files
• src/hg/makeDb/trackDb/human/hgdpFst.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Change reference date from ePub info to print info
• src/hg/makeDb/trackDb/human/hgdpGeo.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Change reference date from ePub info to print info
• src/hg/makeDb/trackDb/human/hgdpHzy.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Change reference date from ePub info to print info
• src/hg/makeDb/trackDb/human/hgdpIhs.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Change reference date from ePub info to print info
• src/hg/makeDb/trackDb/human/hgdpXpehh.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Change reference date from ePub info to print info
• src/hg/makeDb/trackDb/lowelab/acidBott_VIRUS/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_1/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_2/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_3/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_6/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_7/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_8/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
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• src/hg/makeDb/trackDb/lowelab/hydrSp_128_5R1/multizAquificales.html
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• src/hg/makeDb/trackDb/lowelab/hydrSp_128_5R1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/hydrY04A/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/hydrY04A/ultraConserved.html
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• src/hg/makeDb/trackDb/lowelab/hypeButy1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/nanEqu1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/natrMaga0/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/natrPhag_PHICH1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/natrPhar1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/nitrMari1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/picrTorr1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/pyrAby1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/pyrAer1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/pyrFur2/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/pyroAbys_VIRUS_1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/pyroSphe_VIRUS/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/sulfIsla_FILAMENTOUS/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/sulfIsla_ROD_SHAPED_VIRUS_2/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/sulfIsla_Y_G_57_14/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/sulfViru_KAMCHATKA_1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/therAcid1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/therOnnu1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/therPend1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/therSibi1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/therTena1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/therTena_SPHERICAL_VI/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/therVolc1/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/uncuMeth_RCI/trackDb.ra
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• src/hg/makeDb/trackDb/lowelab/vulcDist0/trackDb.ra
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• src/hg/makeDb/trackDb/marmoset/priority.ra
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    primate and mammal chain reordering, etc. reduced some influence of stay priority.ra files
• src/hg/makeDb/trackDb/marmoset/trackDb.ra
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• src/hg/makeDb/trackDb/mouse/mm9/NIAGene.html
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    fixing up the citations
• src/hg/makeDb/trackDb/mouse/mm9/REST.html
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    Renamed into rest.html.
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    Updated the Display section per data provider's request.
• src/hg/makeDb/trackDb/mouse/mm9/rest.html
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    cleaning up lots of loose references
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    adding some links
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    just cutting the lines to 80 chars (no changes)
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• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
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    Added color and altColor for REST.
• src/hg/makeDb/trackDb/mouse/priority.ra
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• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
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    changed name to 0_db for hg18 chainnets
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    fixed accidently breakage of 9way. had interrupted the block when moving nscan override
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    moved override block to bottom of track section
• src/hg/makeDb/trackDb/opossum/priority.ra
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• src/hg/makeDb/trackDb/opossum/trackDb.ra
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    moved priority.ra content into trackDb.ra as overrides
• src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.ra
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    changed short label to o_db for hg18 chainnets
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• src/hg/makeDb/trackDb/orangutan/priority.ra
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• src/hg/makeDb/trackDb/orangutan/trackDb.ra
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• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
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    restoring Human to longLabel on hg18 chain/net tracks
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• src/hg/makeDb/trackDb/rhesus/trackDb.ra
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• src/hg/makeDb/trackDb/squirt/ci1/description.html
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    added the common name of the squirt
• src/hg/makeDb/trackDb/squirt/ci2/description.html
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    added the common name of the squirt
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
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    Updating chainNet composite tracks for tetNig2, fr2, oryLat2, danRer6, hg19, mm9
• src/hg/makeDb/trackDb/trackDb.ra
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    removing comment about possum release alpha
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    Updating chainNet composite tracks for tetNig2, fr2, oryLat2, danRer6, hg19, mm9
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    dropping release alpha for chainNetMonDom5 so it works on beta
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    converted dbChainNet trackNames to chainNetDb to match pattern we've been using
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    converted dbChainNet trackNames to chainNetDb to match pattern we've been using
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    primate and mammal chain reordering, etc. reduced some influence of stay priority.ra files
• src/hg/makeDb/trackDb/transMap.html
  • 1.14 lines changed: 4, context: html, text, full: html, text
    updated transMap doc
• src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra
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    converted dbChainNet trackNames to chainNetDb to match pattern we've been using
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.53 lines changed: 10, context: html, text, full: html, text
    Updating chainNet composite tracks for tetNig2, fr2, oryLat2, danRer6, hg19, mm9
• src/hg/tcga/scripts/segToBed15.py
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    fixed bug with sparse data
• src/hg/utils/automation/Encode.pm
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    New order of the day. DAFs must have dafVersion 1.1
• src/makefile
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    added bigWigInfo program to user apps list
• src/utils/qa/checkTableStatus.csh
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    fixed status dump to work proely for RR
• src/utils/qa/countRows.csh
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    inproved usage and output
• src/utils/qa/findNewTables.csh
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    reversed change to create_time and added GENBANK filter to grep to properly eliminate genbank tables
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    adjusted to use create_time instead of update_time to eliminate genbank from output
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    fixed to deal with MySQL 5.0 status diff
• src/utils/qa/getDbSize.csh
  • 1.13 lines changed: 1, context: html, text, full: html, text
    typo
• src/utils/qa/getRRtableStatus.csh
  • 1.14 lines changed: 2, context: html, text, full: html, text
    inproved usage and output
• src/utils/qa/qaConfig.bash
  • 1.5 lines changed: 1, context: html, text, full: html, text
    added comment about what GENBANK variable is
• src/utils/qa/qaConfig.csh
  • 1.5 lines changed: 1, context: html, text, full: html, text
    added comment about what GENBANK variable is
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.79 lines changed: 2, context: html, text, full: html, text
    v216 preview
• src/utils/qa/weeklybld/buildHgCentralSql.csh
  • 1.18 lines changed: 3, context: html, text, full: html, text
    fixing more mysql 5 dump problems due to not being line-oriented
• src/utils/qa/weeklybld/makeUserApps.csh
  • 1.5 lines changed: 5, context: html, text, full: html, text
    fixing so old gets deleted before copying new to hgdownload

• lines changed: 8550
• files changed: 254