braney: changes by commit

branch to review (2010-03-02 to 2010-03-16) v227

• turn off the nextItem arrows by default for the MethylSeq track
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.897 - lines changed: 1, context: html, text, full: html, text
• fix up some metadata for H9ES cell in MethylSeq
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.898 - lines changed: 1, context: html, text, full: html, text
• change default visible tables for MethylSeq
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.899 - lines changed: 2, context: html, text, full: html, text
• another attempt to capture what's changed between releases. We need a script to make these consistent
  • src/hg/makeDb/doc/encodeDccHg18/uwAffyExonArray.release2.notes.txt 1.1 - lines changed: 95, context: html, text, full: html, text
• add some release notes
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html 1.17 - lines changed: 2, context: html, text, full: html, text
• RikenCage Loc release notes
  • src/hg/makeDb/doc/encodeDccHg18/rikenCage.release2.notes.txt 1.1 - lines changed: 169, context: html, text, full: html, text
• add gencode
  • src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra 1.3 - lines changed: 135, context: html, text, full: html, text
• extract GIS Pet tracks to separte include file
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.alpha.ra 1.1 - lines changed: 1077, context: html, text, full: html, text
• extract GIS RNA-loc to its own file
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.908 - lines changed: 870, context: html, text, full: html, text
• fix a missing color for HeLa rep2 in UwAffyExon trakc
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.921 - lines changed: 1, context: html, text, full: html, text
• add release policy paragram, and release notes
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.html 1.6 - lines changed: 13, context: html, text, full: html, text
• update to understand tri-state release mechanims
  • src/hg/utils/tdbQuery/tdbQuery.c 1.31 - lines changed: 95, context: html, text, full: html, text
• make it so tdbQuery is called with -release option
  • src/hg/makeDb/trackDb/loadTracks 1.20 - lines changed: 1, context: html, text, full: html, text
• a new function
  • src/hg/utils/tdbQuery/tdbRecord.h 1.5 - lines changed: 6, context: html, text, full: html, text
• take out colorByStrand on signal tracks which aren't colored by strand
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.alpha.ra 1.5 - lines changed: 39, context: html, text, full: html, text