Commits for braney

v239_preview to v239_base (2010-08-24 to 2010-08-31) v239

• fix problem with mouse cell types not getting the org right
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 39, context: html, text, full: html, text
• fix a bug where if Jim's regulation multi-wiggles were selected, core was dumped
  • src/hg/hgGenome/import.c - lines changed 2, context: html, text, full: html, text
• is hoping that eventually he can fix this. Need to filter on organism .
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 9, context: html, text, full: html, text
• remove the Alignments view
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra - lines changed 107, context: html, text, full: html, text
• change from bedGraphs to bigWigs
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 196, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra - lines changed 124, context: html, text, full: html, text
• if the color mode is off, default to using the track color specified in trackDb
  • src/hg/hgTracks/bamTrack.c - lines changed 3, context: html, text, full: html, text
• make bamColorMode be off by default so ENCODE cell colors are displayed
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra - lines changed 1, context: html, text, full: html, text
• put fileIndex after fileName in ENCODE "..." stanzas. Make into a download link.
  • src/hg/lib/hui.c - lines changed 2, context: html, text, full: html, text
• take view out of sortOrder since it's not here anymore (fixes (null) header)
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra - lines changed 1, context: html, text, full: html, text
• v239 final build
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• "New version number v239"
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text