Commits for kate

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

• Indicate assembly next to genomic position on item details. refs #15645
  
  • src/hg/hgc/gtexClick.c - lines changed 2, context: html, text, full: html, text
• Add version awareness to tissue handling. refs #15645
  
  • src/hg/hgc/gtexClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/gtexInfo.h - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/gtexTissue.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/gtexGeneBed.c - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/gtexInfo.c - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/gtexTissue.c - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gtexUi.c - lines changed 4, 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/gtex/V6.txt - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtex/hgGtex.c - lines changed 255, 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/gtexClick.c - lines changed 8, context: html, text, full: html, text
  • src/hg/hgc/hgcData/gtexBoxplot.R - lines changed 7, context: html, text, full: html, text
  • src/hg/hgc/hgcData/gtexColorsV4.R - lines changed 64, 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/gtexGeneTcap.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/htdocs/images/gtex/gtexSampleAge.V6.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/htdocs/images/gtex/gtexSampleRin.V6.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/htdocs/images/gtexGeneTcap.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/outside/gtexPlot/README.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/outside/gtexPlot/makeSampleDf.csh - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/gtexPlot/plotSampleAge.R - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/outside/gtexPlot/plotSampleRin.R - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/gtexGeneExpr.html - lines changed 5, context: html, text, full: html, text
• Minor wording change.
  
  • src/hg/makeDb/trackDb/human/gtexGeneExpr.html - lines changed 1, 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/hgTracks/gtexTracks.c - lines changed 24, context: html, text, full: html, text
  • src/hg/inc/gtexGeneBed.h - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/gtexUi.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/gtexGeneBed.c - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/gtexUi.c - lines changed 7, context: html, text, full: html, text
• Merge branch 'gtexCoding'
  
• 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/hgTracks/gtexTracks.c - lines changed 78, context: html, text, full: html, text
  • src/hg/hgc/gtexClick.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/gtexGeneBed.sql - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/gtex.txt - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 1, context: html, text, full: html, text
  • src/inc/sqlList.h - lines changed 3, context: html, text, full: html, text
  • src/lib/sqlList.c - lines changed 20, context: html, text, full: html, text
  • src/lib/tests/makefile - lines changed 4, context: html, text, full: html, text
  • src/lib/tests/testSum.c - lines changed 35, context: html, text, full: html, text
  • src/utils/bedScore/bedScore.c - lines changed 16, context: html, text, full: html, text
• Remove debug statements.
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 3, context: html, text, full: html, text
• Fix compile err.
  
  • src/hg/makeDb/outside/hgGtexExonBed/hgGtexExonBed.c - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c - lines changed 8, context: html, text, full: html, text
• Fix swapped colors.
  
  • src/hg/hgc/hgcData/gtexColorsV4.R - lines changed 4, context: html, text, full: html, text