Commits for kate

v283_base to v284_preview (2013-05-07 to 2013-05-14) v284

• Remove obsolete code (support for 'inputTracksSubgroupDisplay' tsetting/feature, which poked through a tracks and trackDb in a related composite track for info -- to provide more features ??. The code was all bracketed with TO_BE_REMOVED. Alternate approach uses inputTableFieldDisplay setting
  • src/hg/hgc/peakClusters.c - lines changed 221, context: html, text, full: html, text
• Create version of track clustered by target protein. refs #10097
  • src/hg/lib/clusterInputTrackTable3.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/clusterInputTrackTable4.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeRegHg19.txt - lines changed 40, context: html, text, full: html, text
• Create version of track clustered by target protein. refs #10097
  • src/hg/hgc/peakClusters.c - lines changed 87, context: html, text, full: html, text
  • src/hg/lib/clusterInputTrackTable5.sql - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 35, context: html, text, full: html, text
• Fix problem with downloads page column. QA issue 11. refs 10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra - lines changed 1, context: html, text, full: html, text
• Fix short label inconsistencies. QA #14. refs #10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra - lines changed 4, context: html, text, full: html, text
• Clarify protocol in long labels. QA #13. refs #10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra - lines changed 6, context: html, text, full: html, text
• HA-E2F1 now grouped with E2F1, input from Peggy Farnham (USC). refs #10042
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgTfbsUniform.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra - lines changed 5, context: html, text, full: html, text
• Merge branch 'master' into tfclusters
• Uniqify short labels. refs #10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra - lines changed 13, context: html, text, full: html, text
• Added link to Mouse ENCODE portal, by request of Mike Pazin and Bing Ren
  • src/hg/htdocs/ENCODE/index.html - lines changed 12, context: html, text, full: html, text
• Merge branch 'master' into tfclusters
• ENCODE TFBS clusters track update. refs #10097
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 46, context: html, text, full: html, text
• Correct misassignment of IMR90 to tier2 (it's in tier 2.5). refs #10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra - lines changed 6, context: html, text, full: html, text
• 1. Set track defaults (1 'interesting' TF, CTCF, and POL2 for tier1 and tier2, plus a few tier 2.5. refs #10042. Also track setting for factorSource. refs #10097
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra - lines changed 75, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• Adjust TFBS track visibilities. The uniform track shows all labs, so lab-specific tracks can now be hidden by default. refs #10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release4.ra - lines changed 1, context: html, text, full: html, text
• Tweak visibility -- can be hidden now that Uniform TFBS is public. refs #10042
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra - lines changed 1, context: html, text, full: html, text
• Suggestion from JK during code review. Simpler is better
  • src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c - lines changed 1, context: html, text, full: html, text
• Oops, simplification changed functionality -- rolling back
  • src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c - lines changed 1, context: html, text, full: html, text