braney: changes by commit

branch to review (2009-09-29 to 2009-10-06) v217

• new CSHL long RNA-seq setup
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.548 - lines changed: 241, context: html, text, full: html, text
• add append option to add to, rather than create files
  • src/hg/bedSplitOnChrom/bedSplitOnChrom.c 1.4 - lines changed: 7, context: html, text, full: html, text
• put X in missing 14th field
  • src/hg/encode/converters/tagToBed12/tagToBed12.c 1.2 - lines changed: 1, context: html, text, full: html, text
• fix narrowPeak check to actually use the peak rather than the score
  • src/hg/encode/validateFiles/validateFiles.c 1.28 - lines changed: 1, context: html, text, full: html, text
• add color to CSHL Long RNA-seq track
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.549 - lines changed: 4, context: html, text, full: html, text
• take out commented out old CSHL short RNA-seq entries
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.550 - lines changed: 426, context: html, text, full: html, text
• implement Angie's suggestions to make the code more readable
  • src/hg/bedItemOverlapCount/bedItemOverlapCount.c 1.19 - lines changed: 34, context: html, text, full: html, text
• fix up short labels for Affy RNA loc track
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.551 - lines changed: 105, context: html, text, full: html, text
• small fix, npls to nplm in Affy RNA loc track
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.552 - lines changed: 2, context: html, text, full: html, text
• turn on GM12878 nlos by default in Affy RNA loc track
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.553 - lines changed: 4, context: html, text, full: html, text
• colorByStrand for bed12's
  • src/hg/hgTracks/bedTrack.c 1.17 - lines changed: 4, context: html, text, full: html, text
• fix up some long labels for AffyRna and other tracks qVS: ----------------------------------------------------------------------
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.562 - lines changed: 67, context: html, text, full: html, text