larrym: changes by file

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

• src/makefile
  • 1.60 lines changed: 6, context: html, text, full: html, text
    add bedItemOverlapCount and bedExtendRanges to userApps list
• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.10 lines changed: 23, context: html, text, full: html, text
    support host, user and password args
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.60 lines changed: 1, context: html, text, full: html, text
    use pushq B (i.e. to force human review before QA sees the entry)
• src/hg/encode/encodeValidate/test/expected/methylseq/README.txt
  • 1.2 lines changed: 3, context: html, text, full: html, text
    table name changed
• src/hg/encode/encodeValidate/test/expected/methylseq/load.ra
  • 1.3 lines changed: 2, context: html, text, full: html, text
    table name changed
• src/hg/encode/encodeValidate/test/expected/methylseq/trackDb.ra
  • 1.3 lines changed: 20, context: html, text, full: html, text
    table name changed
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.235 lines changed: 2, context: html, text, full: html, text
    fix Methyl27K56 long labels
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • 1.6 lines changed: 94, context: html, text, full: html, text
    cleanup
  • 1.5 lines changed: 30, context: html, text, full: html, text
    cleanup and fix typos
• src/hg/utils/automation/Encode.pm
  • 1.37 lines changed: 1, context: html, text, full: html, text
    add dcc to downloadDir
• src/hg/utils/bedExtendRanges/bedExtendRanges.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    fix typo in usage
  • 1.3 lines changed: 25, context: html, text, full: html, text
    allow user to use remote db (e.g. mysql.cse.ucsc.edu)