Commits for kate

v292_preview to v292_preview2 (2013-10-28 to 2013-11-04) v292

• Start reg motif work with track of Larry's tables. refs #9092
  • src/hg/hgc/hgc.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeRegHg19.txt - lines changed 1, context: html, text, full: html, text
• Start reg motif work with track of Larry's tables. refs #9092
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 10, context: html, text, full: html, text
• Merge branch 'master' into tfMotif
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 51, context: html, text, full: html, text
• Merge branch 'master' into tfMotif
• Enable Larry Meyer's implementation of this feature. refs #9092
  • src/hg/hgTracks/factorSource.c - lines changed 11, context: html, text, full: html, text
  • src/hg/hgc/peakClusters.c - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/txCluster.h - lines changed 3, context: html, text, full: html, text
• Ad position links for motifs within cluster. refs #9092
  • src/hg/hgc/peakClusters.c - lines changed 9, context: html, text, full: html, text
• Merge branch 'master' into tfMotif
  • src/hg/makeDb/doc/encodeRegHg19.txt - lines changed 8, context: html, text, full: html, text
• Add trackDb for 2 motif tracks
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 13, context: html, text, full: html, text
• Enable conditional code and merge
  • src/hg/hgTracks/factorSource.c - lines changed 38, context: html, text, full: html, text
  • src/hg/hgc/peakClusters.c - lines changed 10, context: html, text, full: html, text
• Fix merge conflict
• Merge branch 'master' into tfMotif
• Load track of ENCODE DNase footprints from EBI (ENCODE AWG)
  • src/hg/makeDb/doc/encodeAwgHg19.txt - lines changed 36, context: html, text, full: html, text
• Remove hard-coded tablename for TFBS Motifs
  • src/hg/inc/txCluster.h - lines changed 5, context: html, text, full: html, text
• 1. Add trackDb setting (motifTable) to replace hard-coded table name 2. Lower brightness of green highlight color 3. Add chevrons to peak based on diretionality of motif. refs #9092. TF Motif feature
  • src/hg/hgTracks/factorSource.c - lines changed 34, context: html, text, full: html, text
• TF Motif table setting added to TFBS Clusters. Also adding DNase footprint track which will possibly accompany TFBS clusters with motifs. refs #9092
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwg.ra - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseMaster.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• Display only highest-scoring motif. Conditionally compiled for now (exploring info in multiple hits for now)
  • src/hg/hgTracks/factorSource.c - lines changed 14, context: html, text, full: html, text
• Turn on conditional compilation for highest-scoring only
  • src/hg/hgTracks/factorSource.c - lines changed 1, context: html, text, full: html, text
• 1. Limit motif hit info to highest scoring 2. Move motif score info near Motif panel. 3. Add strand info to motif hit description. refs #9092
  • src/hg/hgc/peakClusters.c - lines changed 44, context: html, text, full: html, text
• Add trackDb setting for motif PWM table. refs #9092
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• Detect problematic motif tables. refs #9092
  • src/hg/hgc/regMotif.c - lines changed 9, context: html, text, full: html, text
• Expand motif info in details top panel. refs #9092
  • src/hg/hgc/peakClusters.c - lines changed 9, context: html, text, full: html, text
• Add link to Motif panel for help page. refs #9092
  • src/hg/hgc/peakClusters.c - lines changed 2, context: html, text, full: html, text
• Add link to Motif panel for help page. refs #9092
  • src/hg/hgc/regMotif.c - lines changed 4, context: html, text, full: html, text
• Fix motif table. refs #9092
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 1, context: html, text, full: html, text
• Merge branch 'master' into tfMotif