Commits for braney

v247_base to v248_preview (2011-02-14 to 2011-02-22) v248

• add cell name to names. This needs to be fixed to use the tag instead of the term to remove the special characters
  • src/hg/encode/docId/docIdSubmitDir/docIdSubmitDir.c - lines changed 4, context: html, text, full: html, text
  • src/hg/encode/docId/docIdView/docIdView.c - lines changed 4, context: html, text, full: html, text
  • src/hg/encode/docId/inc/docId.h - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/docId/lib/docIdSub.c - lines changed 2, context: html, text, full: html, text
• a complicated commit to support the arrows in decipher tracks, next item buttons on bigBeds, and the beginnings of BAM wiggles
  • src/hg/hgTracks/bamTrack.c - lines changed 116, context: html, text, full: html, text
  • src/hg/hgTracks/bedTrack.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/bigBedTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 68, context: html, text, full: html, text
  • src/hg/hgTracks/snakeTrack.c - lines changed 1, context: html, text, full: html, text
• handle bamWigs
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 2, context: html, text, full: html, text
• add a bamWig track
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 10, context: html, text, full: html, text
• add bedRnaElements
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• hmm... thought I'd moved this into place
  • src/hg/encode/autoSql/bedRnaElements.as - lines changed 13, context: html, text, full: html, text
• add an option to do simple checking on input as stop-gap for GTF acceptance in ENCODE pipeline
  • src/hg/utils/gtfToGenePred/gtfToGenePred.c - lines changed 5, context: html, text, full: html, text
• make check for GTF not look into the hierarchy. This is stop-gap until we get GTF validation into validateFiles
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• add an option to convert a '.' into a NULL in the specified field
  • src/hg/makeDb/hgLoadBed/hgLoadBed.c - lines changed 9, context: html, text, full: html, text
• let bedRnaElements have a NULL field
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 5, context: html, text, full: html, text
• add a note about start and end coordinates being in BED format
  • src/utils/bigWigSummary/bigWigSummary.c - lines changed 1, context: html, text, full: html, text
• this is called bedRnaElements.as now
  • src/hg/encode/autoSql/rnaElements.as - lines changed 13, context: html, text, full: html, text
• take out the generic Merge commits
  • src/utils/git-reports/git-reports.c - lines changed 2, context: html, text, full: html, text
• v248 preview
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text