braney: changes by file

review to branch (2010-05-11 to 2010-05-18) v231

• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.224 lines changed: 17, context: html, text, full: html, text
    take out parallel BAM validation path that was broken
• src/hg/hgc/hgc.c
  • 1.1621 lines changed: 1, context: html, text, full: html, text
    change how the two sequences are printed out for split aligns
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.969 lines changed: 2, context: html, text, full: html, text
    move RikenCage includes to the new policy
  • 1.967 lines changed: 5, context: html, text, full: html, text
    add color to H1hesc for GIS RNA-seq
  • 1.965 lines changed: 5, context: html, text, full: html, text
    taking LongPolyA+ out of the sort order and dimensions since it is always set in the data for GIS RNA-seq
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.11 lines changed: 2, context: html, text, full: html, text
    add information about the clustering process
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html
  • 1.8 lines changed: 6, context: html, text, full: html, text
    add some more text about the alignments to describe their color
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.18 lines changed: 2, context: html, text, full: html, text
    change Alignments view to be called Tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.new.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    change alignments view to Tags view
  • 1.1 lines changed: 721, context: html, text, full: html, text
    conform to the threeStateTrackDb naming scheme
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.ra
  • 1.1 lines changed: 699, context: html, text, full: html, text
    conform to the threeStateTrackDb naming scheme
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeBroadChipSeq.ra
  • 1.2 lines changed: 11164, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeChromatinMap.ra
  • 1.2 lines changed: 12139, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeHudsonalphaChipSeq.ra
  • 1.2 lines changed: 16385, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeHudsonalphaRnaSeq.ra
  • 1.3 lines changed: 279, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeUwChIPSeq.ra
  • 1.2 lines changed: 12796, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeUwDGF.ra
  • 1.2 lines changed: 469, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeUwDnaseSeq.ra
  • 1.2 lines changed: 7608, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/wgEncodeYaleChIPseq.ra
  • 1.2 lines changed: 24601, context: html, text, full: html, text
    moved these down into alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • 1.2 lines changed: 1873, context: html, text, full: html, text
    fixed problems with metadata
  • 1.1 lines changed: 0, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
  • 1.1 lines changed: 11164, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBuOrchid.ra
  • 1.2 lines changed: 35, context: html, text, full: html, text
    fixed problems with metadata
  • 1.1 lines changed: 0, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • 1.2 lines changed: 4037, context: html, text, full: html, text
    add metadata from fileDb.ra in download dirs
  • 1.1 lines changed: 3043, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • 1.1 lines changed: 12139, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • 1.1 lines changed: 480, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • 1.1 lines changed: 982, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeDukeAffyExonArray.ra
  • 1.1 lines changed: 1045, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisDnaPet.ra
  • 1.1 lines changed: 579, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra
  • 1.2 lines changed: 825, context: html, text, full: html, text
    add metadata from fileDb.ra in download dirs
  • 1.1 lines changed: 1484, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • 1.1 lines changed: 445, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHelicosRnaSeq.ra
  • 1.1 lines changed: 55, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • 1.1 lines changed: 16385, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra
  • 1.1 lines changed: 103, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethyl27.ra
  • 1.1 lines changed: 97, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
  • 1.1 lines changed: 1611, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaRnaSeq.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    hopefully updating to the right value
  • 1.1 lines changed: 279, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra
  • 1.2 lines changed: 397, context: html, text, full: html, text
    add metadata from fileDb.ra in download dirs
  • 1.1 lines changed: 1044, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSangerGencode.ra
  • 1.2 lines changed: 55, context: html, text, full: html, text
    fixed problems with metadata
  • 1.1 lines changed: 0, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSunyalbanyRnaGeneChip.ra
  • 1.1 lines changed: 134, context: html, text, full: html, text
    new
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • 1.1 lines changed: 12796, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDGF.ra
  • 1.1 lines changed: 469, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • 1.1 lines changed: 7608, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • 1.1 lines changed: 24601, context: html, text, full: html, text
    moved these down from above
• src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra
  • 1.21 lines changed: 1331, context: html, text, full: html, text
    moving this to trackDb.wgEncode.ra
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • 1.1 lines changed: 1331, context: html, text, full: html, text
    moving trackDb.enc.ra to here
• src/hg/makeDb/trackDb/human/hg19/metaDb/wgEncodeHaibTfbs.ra
  • 1.3 lines changed: 1399, context: html, text, full: html, text
    moving these down to the alpha directory
• src/hg/makeDb/trackDb/human/hg19/metaDb/wgEncodeSydhHistone.ra
  • 1.2 lines changed: 467, context: html, text, full: html, text
    moving these down to the alpha directory
• src/hg/makeDb/trackDb/human/hg19/metaDb/wgEncodeSydhTfbs.ra
  • 1.3 lines changed: 2639, context: html, text, full: html, text
    moving these down to the alpha directory
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • 1.1 lines changed: 1399, context: html, text, full: html, text
    add these in the alpha dir
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • 1.1 lines changed: 467, context: html, text, full: html, text
    add these in the alpha dir
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • 1.1 lines changed: 2639, context: html, text, full: html, text
    add these in the alpha dir
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.enc.ra
  • 1.10 lines changed: 423, context: html, text, full: html, text
    moved to trackDb.wgEncode.ra
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.92 lines changed: 1, context: html, text, full: html, text
    moved trackDb.enc.ra to trackDb.wgEncode.ra
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • 1.1 lines changed: 423, context: html, text, full: html, text
    moved from trackDb.enc.ra