Commits for braney

v239_base to v240_preview (2010-08-31 to 2010-09-07) v240

• a couple of changes to Gencode track
  • src/hg/hgc/hgc.c - lines changed 28, context: html, text, full: html, text
• print out level if we have a class table with a level field
  • src/hg/hgc/hgc.c - lines changed 9, context: html, text, full: html, text
• some changes that Katrina requested, version 4 instead of release 4, and taking V4 out of the short table
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.ra - lines changed 1, context: html, text, full: html, text
• more doc
  • src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt - lines changed 32, context: html, text, full: html, text
• do the spacing correctly when there is more than one transcript for an id. I think this only happens on the PAR regions.
  • src/hg/hgc/hgc.c - lines changed 6, context: html, text, full: html, text
• reload classes table with hgLoadSqlTab to get around some munging
  • src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt - lines changed 9, context: html, text, full: html, text
• change 2way_consensus_pseudogene to 2way_pseudogene
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.ra - lines changed 2, context: html, text, full: html, text
• add 2way_pseudogene
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• update to reflect reality, apparently these haven't been used for a while
  • src/hg/inc/gencodeGeneClass.h - lines changed 31, context: html, text, full: html, text
  • src/hg/lib/gencodeGeneClass.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/gencodeGeneClass.c - lines changed 104, context: html, text, full: html, text
  • src/hg/lib/gencodeGeneClass.sql - lines changed 6, context: html, text, full: html, text
• v240 preview
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text