mikep: changes by file

branch to review (2009-03-31 to 2009-04-07) v203

• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.61 lines changed: 8, context: html, text, full: html, text
    try and avoid mysql timeout errors for stuff that takes 14,000 seconds or more
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.173 lines changed: 46, context: html, text, full: html, text
    validate csfasta and csqual files with validateFiles prog
  • 1.172 lines changed: 7, context: html, text, full: html, text
    add quick option to validateFiles
  • 1.171 lines changed: 26, context: html, text, full: html, text
    fix warning on comparison with undefined; add fasta file validation by validateFiles program
• src/hg/encode/validateFiles/validateFiles.c
  • 1.16 lines changed: 26, context: html, text, full: html, text
    option for quick checking of files (1000 lines of each)
  • 1.15 lines changed: 43, context: html, text, full: html, text
    validation of fasta files (single-line of sequence, no quality)
  • 1.14 lines changed: 7, context: html, text, full: html, text
    making code easier to read
• src/hg/lib/encode/broadPeak.sql
  • 1.3 lines changed: 4, context: html, text, full: html, text
    some RNA files are > 4gb
• src/hg/lib/encode/pairedTagAlign.sql
  • 1.3 lines changed: 4, context: html, text, full: html, text
    GIS gDNA PET alignments overflow the 4GB table
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.238 lines changed: 71, context: html, text, full: html, text
    first 3 projects of GIS DNA PET
  • 1.237 lines changed: 1, context: html, text, full: html, text
    GIS RNAseq extra views
  • 1.236 lines changed: 133, context: html, text, full: html, text
    GIS RNAseq initial load
  • 1.231 lines changed: 39, context: html, text, full: html, text
    recovered two wiggle tracks for Affy
  • 1.230 lines changed: 4, context: html, text, full: html, text
    temporary fix to avoid bug with scoreMax being set to anything but 1000
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.19 lines changed: 5, context: html, text, full: html, text
    adding comments about symlinks in htdocs
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.53 lines changed: 2, context: html, text, full: html, text
    v204 preview
• src/utils/qa/weeklybld/coBranch.csh
  • 1.5 lines changed: 1, context: html, text, full: html, text
    useing ssl stuff