braney: changes by file

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

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