Commits for kate

v310_preview2 to v310_base (2014-12-15 to 2015-01-05) v310

• First cut UW DNase tracks for hg38. refs #14353
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text
• Add scores to peaks and hotspots. refs #14353
  • src/hg/makeDb/doc/encode3/hg38_encode2_dnase1.txt - lines changed 166, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/reg.txt - lines changed 264, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 2819, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• Extend ENCODE experiment table tools for more flexibility. Most ENCODE metadata of general interest can be obtained from experiment (without requiring metaDb)
  • src/hg/encode/encodeExp/encodeExp.c - lines changed 15, context: html, text, full: html, text
  • src/hg/inc/encode/encodeExp.h - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/encode/encodeExp.c - lines changed 35, context: html, text, full: html, text
• Extend normalization tool for cluster racks to handle DNase from ENCODE EAP (for hg38). refs #14353
  • src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c - lines changed 25, context: html, text, full: html, text
• Minor corrections
  • src/hg/makeDb/doc/encodeRegHg19.txt - lines changed 3, context: html, text, full: html, text
• DNase Clusters track from UW/ENCODE data mapped to hg38. refs #14353
  • src/hg/makeDb/doc/hg38/reg.txt - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 17, context: html, text, full: html, text
• Add track draft track descriptions and tweak configs. refs #14353
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.html - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 16, 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 46, context: html, text, full: html, text
• Resolve merge conflict
  • src/hg/makeDb/doc/hg38/reg.txt - lines changed 329, context: html, text, full: html, text
• Tweak vis
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 1, context: html, text, full: html, text
• More track config tweaks.
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 96, context: html, text, full: html, text
• Remove unnecessary/wrong pValueFilter and qValueFilter settings that override the *Filter wildcard setting. Note that xxFilter will not be flagged if it's missing from tagTypes. It will inherit settings from *Filter.
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 10, context: html, text, full: html, text
• Fix treatment tag flagged by tdbQuery. Retire pValue filters for now (they don't work with bigBed, but we may want them later). refs #14353
  • src/hg/makeDb/trackDb/human/hg38/uwDnase.ra - lines changed 8, context: html, text, full: html, text