braney: changes by commit

branch to review (2010-05-25 to 2010-06-01) v233

• notes!
  • src/hg/makeDb/doc/encodeDccHg18/wgEncodeCaltechRnaSeq.release2.notes.txt 1.1 - lines changed: 516, context: html, text, full: html, text
• added release alpha to new calTech tracks in Jims enhancer track
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.987 - lines changed: 6, context: html, text, full: html, text
• move BAM specific code inside ifdef
  • src/hg/encode/validateFiles/validateFiles.c 1.43 - lines changed: 190, context: html, text, full: html, text
• move to official names
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.new.ra 1.1 - lines changed: 1537, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra 1.1 - lines changed: 1534, context: html, text, full: html, text
• make calTech include files follow spec
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.988 - lines changed: 2, context: html, text, full: html, text
• moved to official names
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.alpha.ra 1.10 - lines changed: 1537, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.beta.ra 1.5 - lines changed: 1534, context: html, text, full: html, text
• fix makeDownloadslink use the current database rather than defaulting to hg18
  • src/hg/inc/hui.h 1.154 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.295 - lines changed: 6, context: html, text, full: html, text
• add canPack to Mapability track
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra 1.13 - lines changed: 1, context: html, text, full: html, text
• very preliminary
  • src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt 1.1 - lines changed: 25, context: html, text, full: html, text
• fix downloads link for Mapability track
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra 1.14 - lines changed: 1, context: html, text, full: html, text
• move down into hg19
  • src/hg/makeDb/trackDb/human/wgEncodeGencode.html 1.8 - lines changed: 254, context: html, text, full: html, text
• first cut at v4 description page
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html 1.1 - lines changed: 246, context: html, text, full: html, text
• first cut at v4 Gencode genes
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra 1.15 - lines changed: 137, context: html, text, full: html, text
• more load procedures
  • src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt 1.2 - lines changed: 30, context: html, text, full: html, text
• added win to dimensions in mapability track
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.994 - lines changed: 1, context: html, text, full: html, text
• move this from wgEncodeGisPet.alpha.ra
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.ra 1.1 - lines changed: 1048, context: html, text, full: html, text
• moved to wgEncodeGisPet.ra
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.alpha.ra 1.15 - lines changed: 1048, context: html, text, full: html, text
• change wgEncodeGisPet.alpha.ra to wgEncodeGisPet.ra
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.997 - lines changed: 1, context: html, text, full: html, text
• take out beta
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra 1.2 - lines changed: 144, context: html, text, full: html, text
• add parent for public mapability track
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.999 - lines changed: 1, context: html, text, full: html, text
• make a variable bamTypes
  • src/hg/utils/automation/Encode.pm 1.67 - lines changed: 1, context: html, text, full: html, text