All File Changes

v292_preview to v292_preview2 (2013-10-28 to 2013-11-04) v292

• src/hg/encode3/validateManifest/VERSION.TXT
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    adding more requested features to 1.7: 2 new (optional?) columns: technical_replicate and paired_end
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    official release of 1.7 for testing
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 65, context: html, text, full: html, text
    adding more requested features to 1.7: 2 new (optional?) columns: technical_replicate and paired_end
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    changing Error: to ERROR: for consistency.
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    re-arranging some if-clauses for consistency. Making paired_end field required for fastq.
• src/hg/hgTables/filterFields.c
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    Fixing typo that I failed to notice during code review. Symptom wasthat numeric filters weren't applied because their operators didn't
    pass the new cmpReal test.
    fixes #12077
    
• src/hg/hgTables/hal.c
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    ifdef out the HAL parts is USE_HAL isn't defined.
• src/hg/hgTracks/factorSource.c
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    Enable Larry Meyer's implementation of this feature. refs #9092
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    Enable conditional code and merge
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    1. Add trackDb setting (motifTable) to replace hard-coded table name 2. Lower brightness of green highlight color 3. Add chevrons to peak based on diretionality of motif. refs #9092. TF Motif feature
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    Display only highest-scoring motif. Conditionally compiled for now (exploring info in multiple hits for now)
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    Turn on conditional compilation for highest-scoring only
• src/hg/hgc/hgc.c
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    Start reg motif work with track of Larry's tables. refs #9092
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    Integer columns of bigBed+ can have associated URLs (all-integer IDs),and we weren't reporting any formatting issues anyway, so send such
    columns through printIdOrLinks.
    
• src/hg/hgc/peakClusters.c
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    Enable Larry Meyer's implementation of this feature. refs #9092
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    Ad position links for motifs within cluster. refs #9092
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    Enable conditional code and merge
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    1. Limit motif hit info to highest scoring 2. Move motif score info near Motif panel. 3. Add strand info to motif hit description. refs #9092
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    Expand motif info in details top panel. refs #9092
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    Add link to Motif panel for help page. refs #9092
• src/hg/hgc/regMotif.c
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    Detect problematic motif tables. refs #9092
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    Add link to Motif panel for help page. refs #9092
• src/hg/htdocs/FAQ/FAQreleases.html
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    Removing genome-archive links and mentions on our help pages, refs #698
• src/hg/htdocs/Neandertal/index.html
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    Removing genome-archive links and mentions on our help pages, refs #698
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
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    Removing genome-archive links and mentions on our help pages, refs #698
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    Added notes to trackDb documentation to make it clearer when to use the multiWig container. Another note about multiWig not working with dragAndDrop setting, refs #11603
• src/hg/htdocs/goldenPath/mapPlots/arch.html
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    Removing genome-archive links and mentions on our help pages, refs #698
• src/hg/htdocs/goldenPath/mapPlots/cytoguide.html
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    Removing genome-archive links and mentions on our help pages, refs #698
• src/hg/htdocs/goldenPath/mapPlots/cytoprogram.html
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    Removing genome-archive links and mentions on our help pages, refs #698
• src/hg/htdocs/goldenPath/mapPlots/index.html
  • lines changed 1, context: html, text, full: html, text
    Removing genome-archive links and mentions on our help pages, refs #698
• src/hg/htdocs/index.html
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    Removing genome-archive links and mentions on our help pages, refs #698
• src/hg/htdocs/staff.html
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    updating Morgan's description to be a little more specific
• src/hg/htdocs/util.html
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    Changing utility links to DNA and Protein duster to skip redirection step
• src/hg/inc/txCluster.h
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    Enable Larry Meyer's implementation of this feature. refs #9092
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    Remove hard-coded tablename for TFBS Motifs
• src/hg/makeDb/doc/encodeAwgHg19.txt
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    Load track of ENCODE DNase footprints from EBI (ENCODE AWG)
• src/hg/makeDb/doc/encodeRegHg19.txt
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    Start reg motif work with track of Larry's tables. refs #9092
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    Merge branch 'master' into tfMotif
• src/hg/makeDb/doc/hg18.txt
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    phastBias GC-biased gene conversion tracks from Katie and Adam. fixes #11697
• src/hg/makeDb/doc/hg19.txt
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    phastBias GC-biased gene conversion tracks from Katie and Adam. fixes #11697
• src/hg/makeDb/doc/taeGut2.txt
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    lastz run to turkey and lift ensGene from taeGut1 to taeGut2 refs #10272
• src/hg/makeDb/genbank/etc/genbank.conf
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    updated human ccds build number
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    disable maximum number of alignments on braNey1
• src/hg/makeDb/genbank/src/makefile
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    fix removed of incorrect bin directory
• src/hg/makeDb/trackDb/armadillo/dasNov3/description.html
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    Fixing description page links for a small set of species, related to refs #10410
• src/hg/makeDb/trackDb/human/dgvPlus.html
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    Adding reference to DGV track html at request of Jeff at DGV refs #11200
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    pointing to correct chimpOrangMacOrthoTable on snp138
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
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    TF Motif table setting added to TFBS Clusters. Also adding DNase footprint track which will possibly accompany TFBS clusters with motifs. refs #9092
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwg.ra
  • lines changed 26, context: html, text, full: html, text
    TF Motif table setting added to TFBS Clusters. Also adding DNase footprint track which will possibly accompany TFBS clusters with motifs. refs #9092
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseMaster.html
  • lines changed 1, context: html, text, full: html, text
    TF Motif table setting added to TFBS Clusters. Also adding DNase footprint track which will possibly accompany TFBS clusters with motifs. refs #9092
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 10, context: html, text, full: html, text
    Start reg motif work with track of Larry's tables. refs #9092
  • lines changed 51, context: html, text, full: html, text
    Merge branch 'master' into tfMotif
  • lines changed 13, context: html, text, full: html, text
    Add trackDb for 2 motif tracks
  • lines changed 26, context: html, text, full: html, text
    TF Motif table setting added to TFBS Clusters. Also adding DNase footprint track which will possibly accompany TFBS clusters with motifs. refs #9092
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    Add trackDb setting for motif PWM table. refs #9092
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    Fix motif table. refs #9092
• src/hg/makeDb/trackDb/human/phastBias.html
  • lines changed 38, context: html, text, full: html, text
    phastBias GC-biased gene conversion tracks from Katie and Adam. fixes #11697
• src/hg/makeDb/trackDb/human/phastBias.ra
  • lines changed 56, context: html, text, full: html, text
    phastBias GC-biased gene conversion tracks from Katie and Adam. fixes #11697
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    phastBias GC-biased gene conversion tracks from Katie and Adam. fixes #11697
• src/hg/makeDb/trackDb/lancelet/braFlo1/description.html
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    Fixing description page links for a small set of species, related to refs #10410
• src/hg/makeDb/trackDb/pig/susScr2/description.html
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    Fixing description page links for a small set of species, related to refs #10410
• src/hg/makeDb/trackDb/pig/susScr3/description.html
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    Fixing description page links for a small set of species, related to refs #10410
• src/hg/makeDb/trackDb/rabbit/oryCun2/description.html
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    Fixing description page links for a small set of species, related to refs #10410
• src/hg/makeDb/trackDb/sheep/oviAri1/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixing description page links for a small set of species, related to refs #10410
• src/hg/makeDb/trackDb/sheep/oviAri3/description.html
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    Fixing description page links for a small set of species, related to refs #10410
• src/hg/makeDb/trackDb/sloth/choHof1/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixing description page links for a small set of species, related to refs #10410
• src/hg/makeDb/trackDb/stickleback/gasAcu1/description.html
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    Fixing description page links for a small set of species, related to refs #10410
• src/hg/makeDb/trackDb/tagTypes.tab
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    TF Motif table setting added to TFBS Clusters. Also adding DNase footprint track which will possibly accompany TFBS clusters with motifs. refs #9092
  • lines changed 1, context: html, text, full: html, text
    Add trackDb setting for motif PWM table. refs #9092
• src/hg/makeDb/trackDb/urchin/strPur1/description.html
  • lines changed 2, context: html, text, full: html, text
    Fixing description page links for a small set of species, related to refs #10410
• src/hg/makeDb/trackDb/urchin/strPur2/description.html
  • lines changed 2, context: html, text, full: html, text
    Fixing description page links for a small set of species, related to refs #10410
• src/inc/common.mk
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    eliminate bogus debugging sslx and cryptox libraries refs #11899
• src/inc/options.h
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    Negative numbers as arguments to command-line programs using options seemed to be a problem.
• src/lib/bigBed.c
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    Fixing mem leak (for when annoStreamBigBed does lots of queries that run into the maxItems limit).
• src/lib/options.c
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    Negative numbers as arguments to command-line programs using options seemed to be a problem.
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    A couple of things that broke compilation
• src/utils/qa/checkTrackUiLinks.csh
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    working with Matt. added quotes around a variable because echo croaks if a link has and ampersand. renamed a variable to make it more intuitive when reading. added ftp to http in a grep because ftp is not an error code. refs #11809
• src/utils/qa/weeklybld/buildEnv.csh
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    v292 preview2
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
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    remove rhead from email list refs #11966

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• files changed: 79