File Changes for kate

v328_base to v329_preview (2016-02-08 to 2016-02-15) v329

• src/hg/hgTrackUi/hgTrackUi.c
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    How was this working ?
    
• src/hg/hgTracks/gtexTracks.c
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    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
  • lines changed 13, context: html, text, full: html, text
    Fixing merge conflit
    
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    Load GTEx V6 gene table in hg19. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
  • lines changed 9, context: html, text, full: html, text
    Add pseudogene transcript class (colored in dense mode. refs #15645
    
  • lines changed 4, context: html, text, full: html, text
    Adjust GTEx item height when filters are used. refs #15645
    
  • lines changed 5, context: html, text, full: html, text
    Minor cleanup. refs #15645
    
• src/hg/hgc/gtexClick.c
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    Tear out partial C implementation of gene expression boxplot. We will use R. refs #15645
    
  • lines changed 15, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
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    Remove debug statement
    
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    Query for transcript description in version agnostic way to accomodate changes to knownToEnsembl table (hg38 vs hg19)
    
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    Finishing touches to GTEx gene details page. Added link to hgGeneand bent knownGene queries for gene description to handle both hg38 and hg19 conventions. refs #15645
    
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    Suppress links to hgGene when there's no page. Add transcript class and color it. refs #15645
    
• src/hg/hgc/hgcData/gtexBoxplot.R
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    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
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    Widen boxplot a bit so longer sample count labels are readable.
    
• src/hg/inc/gtexGeneBed.h
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    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
• src/hg/inc/gtexInfo.h
  • lines changed 3, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
  • lines changed 4, context: html, text, full: html, text
    Make GTEx V6 the default. refs #16545
    
• src/hg/inc/gtexTranscript.h
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    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/inc/gtexUi.h
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    Add JS to disable/enable GTEx gene track config controls when applicable. refs #15645
    
• src/hg/inc/hCommon.h
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    Finishing touches to GTEx gene details page. Added link to hgGeneand bent knownGene queries for gene description to handle both hg38 and hg19 conventions. refs #15645
    
• src/hg/js/hgTracks.js
  • lines changed 32, context: html, text, full: html, text
    Add apply button to trackUi popup (but suppress in description only page, e.g. from trtrackSearch results). refs #16788
    
• src/hg/js/utils.js
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    Disable (gray out) text label on codon numbering. Disabling the checkbox alone is non-obvious
    
  • lines changed 32, context: html, text, full: html, text
    Add JS to disable/enable GTEx gene track config controls when applicable. refs #15645
    
• src/hg/lib/gtexGeneBed.c
  • lines changed 9, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Make GTEx V6 the default. refs #16545
    
• src/hg/lib/gtexInfo.c
  • lines changed 12, context: html, text, full: html, text
    Support for multiple GTEx releases/versions (to add V6 track). refs #15645
    
  • lines changed 18, context: html, text, full: html, text
    Make GTEx V6 the default. refs #16545
    
• src/hg/lib/gtexTranscript.as
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    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/lib/gtexTranscript.c
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    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/lib/gtexTranscript.sql
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    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/lib/gtexUi.c
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    Fix problem with some tissue color patches on GTEx config pages. refs 15645
    
  • lines changed 45, context: html, text, full: html, text
    Add JS to disable/enable GTEx gene track config controls when applicable. refs #15645
    
  • lines changed 2, context: html, text, full: html, text
    Fix uninitialized cart var in GTEx ui. refs #15645
    
• src/hg/lib/hCommon.c
  • lines changed 7, context: html, text, full: html, text
    Finishing touches to GTEx gene details page. Added link to hgGeneand bent knownGene queries for gene description to handle both hg38 and hg19 conventions. refs #15645
    
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    Disable (gray out) text label on codon numbering. Disabling the checkbox alone is non-obvious
    
• src/hg/lib/makefile
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    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/makeDb/doc/gtex/2014-jan.txt
  • lines changed 2, context: html, text, full: html, text
    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
  • lines changed 218, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/makeDb/doc/gtex/V4.txt
  • lines changed 218, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/makeDb/doc/gtex/V6.txt
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    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 15, context: html, text, full: html, text
    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
  • lines changed 21, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 24, context: html, text, full: html, text
    Update tools to load hg38.
    
• src/hg/makeDb/outside/hgGtex/hgGtex.c
  • lines changed 1, context: html, text, full: html, text
    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
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    Remove preliminary code for new GTEx feature (mean+whiskers on hgTracks) from build tool.
    
• src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c
  • lines changed 38, context: html, text, full: html, text
    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
  • lines changed 82, context: html, text, full: html, text
    Load GTEx V6 gene table in hg19. refs #15645
    
  • lines changed 93, context: html, text, full: html, text
    Update tools to load hg38.
    
• src/hg/makeDb/schema/all.joiner
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    Add GTEx table keys. refs #15645
    
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 48, context: html, text, full: html, text
    Flesh out GTEx track description a bit, and update for V6. Thanks to Parisa for contributions refs #15645
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 9, context: html, text, full: html, text
    1. Load GTEx V6 data. Mods to tools and code to support multiple versions. 2. Use GTEx gene models rather than UCSC canonical
    
  • lines changed 2, context: html, text, full: html, text
    Flesh out GTEx track description a bit, and update for V6. Thanks to Parisa for contributions refs #15645
    
  • lines changed 5, context: html, text, full: html, text
    Make GTEx V6 the default. refs #16545
    
• src/inc/cheapcgi.h
  • lines changed 3, context: html, text, full: html, text
    Add JS to disable/enable GTEx gene track config controls when applicable. refs #15645
    
• src/lib/cheapcgi.c
  • lines changed 9, context: html, text, full: html, text
    Add JS to disable/enable GTEx gene track config controls when applicable. refs #15645