File Changes for kate

v330_preview2.1 to v330_base (2016-03-14 to 2016-03-21) v330

• src/hg/hgTracks/gtexTracks.c
  • lines changed 37, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
  • lines changed 34, context: html, text, full: html, text
    Integrate gene class into GTEx cgi support. refs #15645
    
• src/hg/hgc/gtexClick.c
  • lines changed 4, context: html, text, full: html, text
    Change boxplot to tissue ordering alphabetically, to match hgTracks. Leave in code to sort descending by median score, in case we want to provide that as a user option. refs #15645
    
  • lines changed 11, context: html, text, full: html, text
    Integrate gene class into GTEx cgi support. refs #15645
    
• src/hg/hgc/hgcData/gtexBoxplot.R
  • lines changed 12, context: html, text, full: html, text
    Change boxplot to tissue ordering alphabetically, to match hgTracks. Leave in code to sort descending by median score, in case we want to provide that as a user option. refs #15645
    
• src/hg/inc/gtexGeneBed.h
  • lines changed 20, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Libify gene class. refs #15645
    
• src/hg/inc/gtexTranscript.h
  • lines changed 79, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/lib/gtexGeneBed.as
  • lines changed 2, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/lib/gtexGeneBed.c
  • lines changed 57, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
  • lines changed 30, context: html, text, full: html, text
    Libify gene class. refs #15645
    
• src/hg/lib/gtexGeneBed.sql
  • lines changed 2, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/lib/gtexTranscript.as
  • lines changed 6, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/lib/gtexTranscript.c
  • lines changed 162, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/lib/gtexTranscript.sql
  • lines changed 12, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Removed schema no longer needed for GTEx build. refs #15645
    
• src/hg/makeDb/doc/gtex/V4.txt
  • lines changed 9, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/makeDb/doc/gtex/V6.txt
  • lines changed 10, context: html, text, full: html, text
    Trim sample table
    
  • lines changed 74, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 2, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 33, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
• src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c
  • lines changed 127, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
  • lines changed 11, context: html, text, full: html, text
    New schema for GTEX gene bed file. Removes bogus transcriptId and replaces transcriptClass with geneType. refs #15645
    
• src/hg/makeDb/trackDb/human/gtexGeneExprV4.html
  • lines changed 44, context: html, text, full: html, text
    Preserve V4 track description. refs #15645
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 32, context: html, text, full: html, text
    A little cleanup to trackDb. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Change strategy for assigning gene class. Replacing transcript class in table with GENCODE gene type (from latest GENCODE attributes file), and using this to derive a class during display. TODO: change gtexGeneBed schema to reflect this. refs #15645
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    A little cleanup to trackDb. refs #15645