Commits for kate

v312_base to v313_preview (2015-02-16 to 2015-02-23) v313

• Refer to local ENCODE page. refs #14353
  
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/uwDnaseClusters.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/uwDnaseSignal.html - lines changed 2, context: html, text, full: html, text
• Testing for data issue
  
  • src/hg/makeDb/doc/hg38/reg.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 10, context: html, text, full: html, text
• Merge branch 'master' into dnase38
  
  • src/hg/makeDb/doc/hg38/reg.txt - lines changed 12, context: html, text, full: html, text
• Fix bad loop over input field meta tables
  
  • src/hg/lib/hui.c - lines changed 10, context: html, text, full: html, text
• Add table with info about ENCODE treatment terms (from cv.ra). refs #14353
  
  • src/hg/lib/encode/wgEncodeTreatment.as - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/encode/wgEncodeTreatment.sql - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/reg.txt - lines changed 23, context: html, text, full: html, text
• Add treatment vocab table
  
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 1, context: html, text, full: html, text
• Eliminate unneeded duplicate tables. refs #14353
  
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 95, context: html, text, full: html, text
• Prep for renames. refs #14353
  
  • src/hg/makeDb/doc/hg38/reg.txt - lines changed 40, context: html, text, full: html, text
• Merge branch 'master' into dnase38
  
• Renames to fix poor name choice (meta->vocab). refs #14353
  
  • src/hg/hgc/peakClusters.c - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 24, context: html, text, full: html, text
• Fix vocab setting. refs #14353
  
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 1, context: html, text, full: html, text
• Renames to fix poor name choice (meta->vocab). refs #14353
  
  • src/hg/lib/hui.c - lines changed 3, context: html, text, full: html, text
• Renames to distinguish ENCODE cv from non-ENCODE table-based vocabularies. refs #14353
  
  • src/hg/lib/hui.c - lines changed 5, context: html, text, full: html, text
• Readability changes
  
  • src/hg/lib/hui.c - lines changed 9, context: html, text, full: html, text
• Use controlledVocabulary setting for non-ENCODE (table-based) vocabularies (replace briefly used *MetaTables settings)
  
  • src/hg/hgc/peakClusters.c - lines changed 9, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 6, context: html, text, full: html, text
• First cut loader of GTEX gene track. Enough here to test track display. refs #13504
  
  • src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c - lines changed 242, context: html, text, full: html, text
• First cut loader of GTEX gene track. Enough here to test track display. refs #13504
  
  • src/hg/inc/gtexGeneBed.h - lines changed 71, context: html, text, full: html, text
  • src/hg/lib/gtexGeneBed.as - lines changed 15, context: html, text, full: html, text
  • src/hg/lib/gtexGeneBed.c - lines changed 212, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtexGeneBed/makefile - lines changed 4, context: html, text, full: html, text
• Libify graphics routine used for GTEX bar graph display. refs #13504
  
  • src/hg/inc/hvGfx.h - lines changed 26, context: html, text, full: html, text
• Compute max score, will need this in trackDb. refs #13504
  
  • src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c - lines changed 8, context: html, text, full: html, text
• Libify graphics routine used for GTEX bar graph display. refs #13504
  
  • src/hg/oneShot/tryGtexBoxPlot/tryGtexBoxPlot.c - lines changed 29, context: html, text, full: html, text
• Merge branch 'gtex'
  
• Rename tables for consistency with hg19. refs #14353
  
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 868, context: html, text, full: html, text
• Rename tables for consistency with hg19. refs #14353
  
  • src/hg/makeDb/doc/hg38/reg.txt - lines changed 134, context: html, text, full: html, text
• A little more flexibility with table naming. refs #14731
  
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text
• Change default ordering of views (Peak, Hotspot, Signal). refs #14733
  
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 290, context: html, text, full: html, text
• Move new DNase tracks to ENCODE Reg supertrack. Compare to CHris' lifted track. refs #14353
  
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.html - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 3246, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/uwDnaseClusters.html - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/uwDnaseSignal.html - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.html - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra - lines changed 3243, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnaseClustered.html - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnaseSignal.html - lines changed 45, context: html, text, full: html, text
• Move new DNase tracks to ENCODE Reg supertrack. Compare to CHris' lifted track. refs #14353
  
  • src/hg/makeDb/doc/hg38/reg.txt - lines changed 26, context: html, text, full: html, text
• More renames for consistency with hg19. refs #14353
  
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra - lines changed 21, context: html, text, full: html, text
• Merge branch 'dnase38'
  
• Tweak DNase lifted track config.
  
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra - lines changed 23, context: html, text, full: html, text
• Tweak priorities and label.
  
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra - lines changed 3, context: html, text, full: html, text
• Label tweak.
  
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra - lines changed 1, context: html, text, full: html, text
• Tweak pri
  
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra - lines changed 1, context: html, text, full: html, text