File Changes for kate

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

• src/hg/hgTracks/factorSource.c
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    Enable Larry Meyer's implementation of this feature. refs #9092
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    Enable conditional code and merge
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    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
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    Display only highest-scoring motif. Conditionally compiled for now (exploring info in multiple hits for now)
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    Turn on conditional compilation for highest-scoring only
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    Start reg motif work with track of Larry's tables. refs #9092
• src/hg/hgc/peakClusters.c
  • lines changed 3, context: html, text, full: html, text
    Enable Larry Meyer's implementation of this feature. refs #9092
  • lines changed 9, context: html, text, full: html, text
    Ad position links for motifs within cluster. refs #9092
  • lines changed 10, context: html, text, full: html, text
    Enable conditional code and merge
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    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
  • lines changed 9, context: html, text, full: html, text
    Expand motif info in details top panel. refs #9092
  • 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 9, context: html, text, full: html, text
    Detect problematic motif tables. refs #9092
  • lines changed 4, context: html, text, full: html, text
    Add link to Motif panel for help page. refs #9092
• src/hg/inc/txCluster.h
  • lines changed 3, context: html, text, full: html, text
    Enable Larry Meyer's implementation of this feature. refs #9092
  • lines changed 5, context: html, text, full: html, text
    Remove hard-coded tablename for TFBS Motifs
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 36, context: html, text, full: html, text
    Load track of ENCODE DNase footprints from EBI (ENCODE AWG)
• 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
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    Merge branch 'master' into tfMotif
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, 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/wgEncodeAwg.ra
  • lines changed 26, 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/wgEncodeAwgDnaseMaster.html
  • lines changed 1, 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/wgEncodeReg.ra
  • lines changed 10, context: html, text, full: html, text
    Start reg motif work with track of Larry's tables. refs #9092
  • lines changed 51, context: html, text, full: html, text
    Merge branch 'master' into tfMotif
  • lines changed 13, context: html, text, full: html, text
    Add trackDb for 2 motif tracks
  • lines changed 26, 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
  • lines changed 1, context: html, text, full: html, text
    Add trackDb setting for motif PWM table. refs #9092
  • lines changed 1, context: html, text, full: html, text
    Fix motif table. refs #9092
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, 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
  • lines changed 1, context: html, text, full: html, text
    Add trackDb setting for motif PWM table. refs #9092