All File Changes

v329_preview2 to v329_base (2016-02-22 to 2016-02-29) v329

• src/hg/expMatrixToJson/expMatrixToJson.c
  • lines changed 15, context: html, text, full: html, text
    Fixing a bug with the top 10 genes feature, refs #16341
    
• src/hg/hgTracks/bedTrack.c
  • lines changed 1, context: html, text, full: html, text
    refs #16860. Fixes bug detected with clinGen track which caused it to go through a previously untested code path. Luckily the fix was simply filling in the missing chrom name in a structure.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    refs #16860. Fixes bug in index order. I thought that knownGene might be immune to the need for sorting, but that was wrong after we switched to handling as single chromosomes, which adds a where chrom= clause which triggers mysql to use some other index which disturbs the order of rows returned.
    
  • lines changed 384, context: html, text, full: html, text
    Removing DEBUG warnings from hgTracks multi-region code.
    
• src/hg/hgTracks/rmskJoinedTrack.c
  • lines changed 7, context: html, text, full: html, text
    Removing DEBUG warnings from hgTracks multi-region code.
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 128, context: html, text, full: html, text
    Removing DEBUG warnings from hgTracks multi-region code.
    
  • lines changed 27, context: html, text, full: html, text
    Fixes #16906. Because composite tracks were flipping between different vis values in an unpredictable way, we have stopped trying to free spaceSavers with old vis values.
    
• src/hg/hgc/gtexClick.c
  • lines changed 3, context: html, text, full: html, text
    Don't show transcript ID on GTEx details page. It is somewhat bogus (the actual gene model is a union, and the transcript ID is identified solely to obtain a transcript class. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Cosmetics
    
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 5, context: html, text, full: html, text
    Adding comment about BLAT min lucky match to FAQ, refs #12166
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    Fixing bad url, no RM
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 4, context: html, text, full: html, text
    Updating reference for 2016 NAR Update paper. no redmine.
    
  • lines changed 26, context: html, text, full: html, text
    moving paper to new 2016 section. no redmine.
    
• src/hg/htdocs/images/Galeopterus_variegatus.jpg
  • lines changed 0, context: html, text, full: html, text
    photo for galVar1 from Wikipedia Commons Lip Kee Yap no redmine
    
• src/hg/htdocs/images/gtexGeneTcap.png
  • lines changed 0, context: html, text, full: html, text
    Expand methods and refs, clarify conventions in GTEx gene track description. refs #15645
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v329
    
• src/hg/js/autocomplete.js
  • lines changed 2, context: html, text, full: html, text
    autocomplete.js can't assume that the global hgTracks object exists since it's also used by hgGateway. Thanks Christopher Lee for catching this.
    refs #16892
    
• src/hg/js/hgTracks.js
  • lines changed 4, context: html, text, full: html, text
    Close UI dialog popup if track set to hidden. refs #16788. Note #15
    
  • lines changed 32, context: html, text, full: html, text
    Removing DEBUG warnings from hgTracks.js multi-region code.
    
• src/hg/lib/cart.c
  • lines changed 6, context: html, text, full: html, text
    address #16850
    
• src/hg/lib/fishClones.as
  • lines changed 4, context: html, text, full: html, text
    Updating the table description for fishClones track, refs #15522
    
• src/hg/makeDb/doc/ce11/ws245Genes.txt
  • lines changed 23, context: html, text, full: html, text
    document ws245Gene track construction refs #15209
    
• src/hg/makeDb/doc/gorGor4/initialBuild.txt
  • lines changed 1, context: html, text, full: html, text
    Fixing year in doc entry, refs #16220
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 193, context: html, text, full: html, text
    temporary change to only align human mouse and ailMel1
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    Adding in the all.joiner connections for the fishClones to RP11 and CTD, refs #15522
    
  • lines changed 2, context: html, text, full: html, text
    Setting dupeOk for fishClones-cloneEnd relationship. Making comment more descriptive. refs #15522
    
  • lines changed 19, context: html, text, full: html, text
    Adding trackDb stanzas, all.joiner identifiers and html files for snp146
    tracks in hg19 and hg38.
    refs #16777
    
• src/hg/makeDb/trackDb/fishClones.html
  • lines changed 7, context: html, text, full: html, text
    updating sentence about where we got the fishClones data, refs #15522
    
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 100, context: html, text, full: html, text
    Expand methods and refs, clarify conventions in GTEx gene track description. refs #15645
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    some more tweaks to CRAM support
    
  • lines changed 6, context: html, text, full: html, text
    Fixing typo for hg19 ORegAnno tdb, removing pennant for updated release
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch6.html
  • lines changed 5, context: html, text, full: html, text
    Changing table format, rewording References section, refs #16648
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 31, context: html, text, full: html, text
    Reverting to the hg19 ENCODE color scheme, refs #16844
    
• src/hg/makeDb/trackDb/human/snp146.html
  • lines changed 36, context: html, text, full: html, text
    Adding trackDb stanzas, all.joiner identifiers and html files for snp146
    tracks in hg19 and hg38.
    refs #16777
    
• src/hg/makeDb/trackDb/human/snp146.shared.html
  • lines changed 470, context: html, text, full: html, text
    Adding trackDb stanzas, all.joiner identifiers and html files for snp146
    tracks in hg19 and hg38.
    refs #16777
    
• src/hg/makeDb/trackDb/human/snp146Common.html
  • lines changed 28, context: html, text, full: html, text
    Adding trackDb stanzas, all.joiner identifiers and html files for snp146
    tracks in hg19 and hg38.
    refs #16777
    
• src/hg/makeDb/trackDb/human/snp146Flagged.html
  • lines changed 29, context: html, text, full: html, text
    Adding trackDb stanzas, all.joiner identifiers and html files for snp146
    tracks in hg19 and hg38.
    refs #16777
    
• src/hg/makeDb/trackDb/human/snp146Mult.html
  • lines changed 25, context: html, text, full: html, text
    Adding trackDb stanzas, all.joiner identifiers and html files for snp146
    tracks in hg19 and hg38.
    refs #16777
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 118, context: html, text, full: html, text
    Adding trackDb stanzas, all.joiner identifiers and html files for snp146
    tracks in hg19 and hg38.
    refs #16777
    
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    some more tweaks to CRAM support
    
• src/hg/makeDb/trackDb/tetraodon/tetNig1/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixing bad url, no RM
    
• src/hg/makeDb/trackDb/tetraodon/tetNig2/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixing bad url, no RM
    
• src/hg/makeDb/trackDb/worm/ce11/description.html
  • lines changed 2, context: html, text, full: html, text
    Updating links on ce11 gateway desc page. Turning ce11 gap track off by default, refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Updating links on ce11 gateway desc page. Turning ce11 gap track off by default, refs #15209
    
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 6, context: html, text, full: html, text
    don't CDS status to none for non-coding transcripts
    
• src/hg/utils/gff3ToGenePred/tests/expected/geneDefaultStatusUnknownTest.gp
  • lines changed 5, context: html, text, full: html, text
    added -defaultCdsStatusToUnknown option to default CDS status to unknown rather than complete
    
• src/hg/utils/gff3ToGenePred/tests/expected/geneTranscriptTest.gp
  • lines changed 3, context: html, text, full: html, text
    don't CDS status to none for non-coding transcripts
    
• src/hg/utils/gff3ToGenePred/tests/expected/minimalGenesTest.gp
  • lines changed 9, context: html, text, full: html, text
    don't CDS status to none for non-coding transcripts
    
• src/hg/utils/gff3ToGenePred/tests/expected/noGeneMRnaTest.gp
  • lines changed 2, context: html, text, full: html, text
    don't CDS status to none for non-coding transcripts
    
• src/hg/utils/gff3ToGenePred/tests/expected/noIdTest.gp
  • lines changed 3, context: html, text, full: html, text
    don't CDS status to none for non-coding transcripts
    
• src/lib/bamFile.c
  • lines changed 6, context: html, text, full: html, text
    some more tweaks to CRAM support
    
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding new updateTimesDb.sh script to makefile and removing old script, refs #16553
    
• src/utils/qa/updateTimesDb.sh
  • lines changed 17, context: html, text, full: html, text
    Add check to see if table update times are differen, and if so, output a little marker next the table. Update command line options so they don't accidentally stomp on each other, suggest in CR. Explain table list file names, suggested in CR. refs #16553 #16869
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v329 final build refs #16821
    
• src/utils/tawk
  • lines changed 5, context: html, text, full: html, text
    Adding tawk - awk with FS and OFS set to tab; an old script of ours that wasn't in the tree, refs #16865
    

• lines changed: 1827
• files changed: 55