All File Changes

v330_base to v331_preview (2016-03-21 to 2016-03-28) v331

• confs/hgwbeta.hg.conf
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    Installing updated hg.conf files from UCSC servers
    
• src/hg/checkHgFindSpec/checkHgFindSpec.c
  • lines changed 2, context: html, text, full: html, text
    fix up hgFind issues with genbank meta tables #16809
    
• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/kallistoOnFastqMani
  • lines changed 21, context: html, text, full: html, text
    Fixing up the single end kallisto commands, refs #16244
    
• src/hg/expMatrixClustersForDendrogram/expMatrixClustersForDendrogram.c
  • lines changed 11, context: html, text, full: html, text
    changing the white to black rainbow to be called greyscale as suggested by Jim, refs #16216
    
• src/hg/hgGene/hgGeneData/Human/hg19/links.ra
  • lines changed 1, context: html, text, full: html, text
    Updating a link in hgGene for Wikipedia redirect refs #17052
    
• src/hg/hgGene/hgGeneData/Human/hg38/links.ra
  • lines changed 1, context: html, text, full: html, text
    Updating a link in hgGene for Wikipedia redirect refs #17052
    
• src/hg/hgGene/hgGeneData/links.ra
  • lines changed 1, context: html, text, full: html, text
    Updating a link in hgGene for Wikipedia redirect refs #17052
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 24, context: html, text, full: html, text
    Add checkbox to limit to protein coding genes (I keep wanting this option during testing.). refs #15645
    
  • lines changed 78, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Remove debug statements.
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    Fixes #17063. next/prev exon link should stop at coding region too moving in both directions and on both strands. Previously it was missing half of the tallStart/End behavior.
    
• src/hg/hgc/gtexClick.c
  • lines changed 2, context: html, text, full: html, text
    Indicate assembly next to genomic position on item details. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
  • lines changed 8, context: html, text, full: html, text
    Readability improvements to gene details page boxplot. Use long labels instead of short. Space out sample counts. Change yellow text to black. refs #15645
    
  • lines changed 2, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/hg/hgc/hgcData/gtexBoxplot.R
  • lines changed 7, context: html, text, full: html, text
    Readability improvements to gene details page boxplot. Use long labels instead of short. Space out sample counts. Change yellow text to black. refs #15645
    
• src/hg/hgc/hgcData/gtexColorsV4.R
  • lines changed 64, context: html, text, full: html, text
    Readability improvements to gene details page boxplot. Use long labels instead of short. Space out sample counts. Change yellow text to black. refs #15645
    
  • lines changed 4, context: html, text, full: html, text
    Fix swapped colors.
    
• src/hg/htdocs/ENCODE/index.html
  • lines changed 22, context: html, text, full: html, text
    Adding text requested from SAB Tim Hubbard re: ENCODE portal & UCSC data dates
    
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 4, context: html, text, full: html, text
    added aptMan1 credits and FAQ release info
    
  • lines changed 1, context: html, text, full: html, text
    Updating version info in C. elegans announcement and in FAQ, refs #15209
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 39, context: html, text, full: html, text
    added aptMan1 credits and FAQ release info
    
  • lines changed 2, context: html, text, full: html, text
    added missing bullet point and link to brown kiwi credits
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 77, context: html, text, full: html, text
    Adding announcement for ce11 and aptMan1. Staging announcement for Lens Patent track. refs #15209 #16029
    
  • lines changed 10, context: html, text, full: html, text
    Updating version info in C. elegans announcement and in FAQ, refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    Correcting minor mistakes in annoucement. no redmine.
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 11, context: html, text, full: html, text
    Adding Angie's Data Integrator hgVai paper to pubs page
    
  • lines changed 84, context: html, text, full: html, text
    Added 3 new pubs and updated several existing entries.
    
  • lines changed 10, context: html, text, full: html, text
    Added Lowe et al. pub.
    
  • lines changed 10, context: html, text, full: html, text
    Added Novak et al. pub.
    
• src/hg/htdocs/images/gtex/gtexGeneTcap.png
  • lines changed 0, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/htdocs/images/gtex/gtexSampleAge.V6.png
  • lines changed 0, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/htdocs/images/gtex/gtexSampleRin.V6.png
  • lines changed 0, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/htdocs/images/gtexGeneTcap.png
  • lines changed 0, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/htdocs/indexNews.html
  • lines changed 132, context: html, text, full: html, text
    Adding announcement for ce11 and aptMan1. Staging announcement for Lens Patent track. refs #15209 #16029
    
  • lines changed 4, context: html, text, full: html, text
    Fixing links to credits page in ce11 and aptMan1 announcement, refs #15209 #16029
    
  • lines changed 12, context: html, text, full: html, text
    Updating version info in C. elegans announcement and in FAQ, refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    Correcting minor mistakes in annoucement. no redmine.
    
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    changed to better link for Kentucky meeting
    
  • lines changed 1, context: html, text, full: html, text
    changed to better link for Japan meeting
    
  • lines changed 2, context: html, text, full: html, text
    oops. shoulda tested before committing. added http to Japan link. improved link for ESHG
    
• src/hg/inc/gtexGeneBed.h
  • lines changed 3, context: html, text, full: html, text
    Add checkbox to limit to protein coding genes (I keep wanting this option during testing.). refs #15645
    
• src/hg/inc/gtexInfo.h
  • lines changed 3, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
• src/hg/inc/gtexTissue.h
  • lines changed 2, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
• src/hg/inc/gtexUi.h
  • lines changed 4, context: html, text, full: html, text
    Add checkbox to limit to protein coding genes (I keep wanting this option during testing.). refs #15645
    
• src/hg/lib/gtexGeneBed.c
  • lines changed 8, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
  • lines changed 5, context: html, text, full: html, text
    Add checkbox to limit to protein coding genes (I keep wanting this option during testing.). refs #15645
    
• src/hg/lib/gtexGeneBed.sql
  • lines changed 2, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/hg/lib/gtexInfo.c
  • lines changed 8, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
• src/hg/lib/gtexTissue.c
  • lines changed 7, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
• src/hg/lib/gtexUi.c
  • lines changed 4, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
  • lines changed 7, context: html, text, full: html, text
    Add checkbox to limit to protein coding genes (I keep wanting this option during testing.). refs #15645
    
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    fix up hgFind issues with genbank meta tables #16809
    
• src/hg/lib/hgFind.c
  • lines changed 29, context: html, text, full: html, text
    fix up hgFind issues with genbank meta tables #16809
    
• src/hg/makeDb/doc/gtex/V6.txt
  • lines changed 30, context: html, text, full: html, text
    Reloaded gtexSampleData to restore zero-valued rows so details page boxplot has all data (o/w need special code for missing data). Extend parser to create median tables by gender to speed up gender diffs feature (changes also needed to hgGtexGeneBed and hgTracks to use these). refs #15645
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 54, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 45, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
  • lines changed 1, context: html, text, full: html, text
    Updating a link in hgGene for Wikipedia redirect refs #17052
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes15.csh
  • lines changed 1, context: html, text, full: html, text
    Updating a link in hgGene for Wikipedia redirect refs #17052
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.sh
  • lines changed 1, context: html, text, full: html, text
    Updating a link in hgGene for Wikipedia redirect refs #17052
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 60, context: html, text, full: html, text
    delete xenoMrna from the 53 assemblies for which it hasn't been looked
    at in 2016.
    
• src/hg/makeDb/outside/gtexPlot/README.txt
  • lines changed 16, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/makeDb/outside/gtexPlot/makeSampleDf.csh
  • lines changed 2, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/makeDb/outside/gtexPlot/plotSampleAge.R
  • lines changed 54, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/makeDb/outside/gtexPlot/plotSampleRin.R
  • lines changed 43, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/makeDb/outside/hgGtex/hgGtex.c
  • lines changed 255, context: html, text, full: html, text
    Reloaded gtexSampleData to restore zero-valued rows so details page boxplot has all data (o/w need special code for missing data). Extend parser to create median tables by gender to speed up gender diffs feature (changes also needed to hgGtexGeneBed and hgTracks to use these). refs #15645
    
• src/hg/makeDb/outside/hgGtexExonBed/hgGtexExonBed.c
  • lines changed 8, context: html, text, full: html, text
    Fix compile err.
    
• src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c
  • lines changed 8, context: html, text, full: html, text
    Fix compile err.
    
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Updating release tags for Lens Patents tracks on hg19, mm10, eboVir3, refs #14486
    
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 5, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Minor wording change.
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 1, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Updating release tags for Lens Patents tracks on hg19, mm10, eboVir3, refs #14486
    
• src/hg/makeDb/trackDb/patSeq.html
  • lines changed 8, context: html, text, full: html, text
    Rewording based on CR. Some other minor wording changes to patSeq description page, refs #14486 #17041
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Updating release tags for Lens Patents tracks on hg19, mm10, eboVir3, refs #14486
    
• src/hg/makeDb/trackDb/worm/ce11/cons26way.html
  • lines changed 1, context: html, text, full: html, text
    updating version on conservation track description page, refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/description.html
  • lines changed 4, context: html, text, full: html, text
    Rewording based on CR. Some other minor wording changes to patSeq description page, refs #14486 #17041
    
  • lines changed 10, context: html, text, full: html, text
    Changing assembly version info on gateway description page. Changing WS245 Genes track description page. refs #15209
    
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Minor correction to WS245 Genes longLabel, refs #15209
    
• src/hg/makeDb/trackDb/worm/ws245Genes.html
  • lines changed 9, context: html, text, full: html, text
    Changing assembly version info on gateway description page. Changing WS245 Genes track description page. refs #15209
    
• src/inc/rainbow.h
  • lines changed 1, context: html, text, full: html, text
    changing the white to black rainbow to be called greyscale as suggested by Jim, refs #16216
    
• src/inc/sqlList.h
  • lines changed 3, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/lib/rainbow.c
  • lines changed 3, context: html, text, full: html, text
    changing the white to black rainbow to be called greyscale as suggested by Jim, refs #16216
    
• src/lib/sqlList.c
  • lines changed 20, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/lib/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/lib/tests/testSum.c
  • lines changed 35, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/utils/bedScore/bedScore.c
  • lines changed 16, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v331 preview1
    
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
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    remove steve add mspeir to email refs #16963
    
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 1, context: html, text, full: html, text
    remove steve add mspeir to email refs #16963
    
• src/utils/qa/weeklybld/doNewReview.csh
  • lines changed 1, context: html, text, full: html, text
    remove steve add mspeir to email refs #16963
    
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 1, context: html, text, full: html, text
    remove steve add mspeir to email refs #16963
    
• src/utils/qa/weeklybld/sendLogEmail.pl
  • lines changed 3, context: html, text, full: html, text
    fixup return email and subject line refs #17039
    

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• files changed: 93