kuhn: changes by file

branch to review (2009-05-12 to 2009-05-19) v206

• src/utils/qa/alertBqueue.csh
  • 1.10 lines changed: 12, context: html, text, full: html, text
    improved debugging a little and fixed the case where larrym was being converted to larrymm by adding a space after the substitution
• src/utils/qa/backupCentral.csh
  • 1.14 lines changed: 1, context: html, text, full: html, text
    made dir group writeable
• src/utils/qa/catchBot.csh
  • 1.20 lines changed: 1, context: html, text, full: html, text
    fixed a parameter to sort that was throwing an error
• src/utils/qa/checkBOT.csh
  • 1.13 lines changed: 5, context: html, text, full: html, text
    removed sessionIDs to expose IP itself for getting location of user
• src/utils/qa/checkCoverage.csh
  • 1.9 lines changed: 43, context: html, text, full: html, text
    refactored handling of single chrom. removed extra steps in txStart-assignment pipe. put all rm statements together using else clause. thanks, brooke
• src/utils/qa/checkSync.csh
  • 1.17 lines changed: 1, context: html, text, full: html, text
    put quotes around rm *.out to get rid of annoying error message
• src/utils/qa/compareWholeColumn.csh
  • 1.10 lines changed: 1, context: html, text, full: html, text
    dropped commas in usage statement to conform to norm
• src/utils/qa/copyExtSeqRows.csh
  • 1.6 lines changed: 10, context: html, text, full: html, text
    a few cosmetic or typo changes
• src/utils/qa/countPerChrom.csh
  • 1.8 lines changed: 65, context: html, text, full: html, text
    made it work for RR. allowed optional arguments to be used singly. allowed use of hgwbeta or hgsqlbeta. simplified logic for doing randoms last. removed tableName variable
• src/utils/qa/getChromFieldName.csh
  • 1.4 lines changed: 1, context: html, text, full: html, text
    added exit after error detect. thanks, brooke.
• src/utils/qa/getSplit.csh
  • 1.12 lines changed: 11, context: html, text, full: html, text
    reset to accept hgwbeta as input. dropped machineName checking as redundant. thanks, brooke
  • 1.11 lines changed: 1, context: html, text, full: html, text
    dropped declaration of varialbe no longer used
  • 1.10 lines changed: 25, context: html, text, full: html, text
    simplified and dropped some variables. caught error state where table does not exist either split or unsplit