markd: changes by file

review to branch (2009-11-17 to 2009-12-01) v220

• src/hg/makeDb/genbank/etc/ignore.idx
  • 1.98 lines changed: 175, context: html, text, full: html, text
    added ignore entries
• src/hg/makeDb/trackDb/chicken/galGal3/caCondor454.html
  • 1.1 lines changed: 88, context: html, text, full: html, text
    added CA condor 454 transcript tracks
• src/hg/makeDb/trackDb/chicken/galGal3/trackDb.ra
  • 1.13 lines changed: 15, context: html, text, full: html, text
    added CA condor 454 transcript tracks
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • 1.42 lines changed: 13, context: html, text, full: html, text
    converted uwFootprints to composite track
• src/hg/ratStuff/mafFilter/mafFilter.c
  • 1.15 lines changed: 22, context: html, text, full: html, text
    added option to filter mafs by species prefix
  • 1.14 lines changed: 1, context: html, text, full: html, text
    allow mafFilter -needComp to work on files produced by mafFrag that have species but not sequence in the name
• src/hg/utils/makefile
  • 1.18 lines changed: 2, context: html, text, full: html, text
    added missing wigBedToStep to make
  • 1.17 lines changed: 4, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/makefile
  • 1.1 lines changed: 25, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/refSeqGet.c
  • 1.2 lines changed: 14, context: html, text, full: html, text
    added CDS to meta data
  • 1.1 lines changed: 274, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/refSeqVerInfo.c
  • 1.2 lines changed: 4, context: html, text, full: html, text
    fixed error detected in optimized compile
  • 1.1 lines changed: 152, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/refSeqVerInfo.h
  • 1.1 lines changed: 27, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/makefile
  • 1.1 lines changed: 35, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/basicListTest.gp
  • 1.1 lines changed: 5, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/basicListTest.meta
  • 1.2 lines changed: 4, context: html, text, full: html, text
    added CDS to meta data
  • 1.1 lines changed: 6, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/basicListTest.prot.fa
  • 1.1 lines changed: 20, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/basicListTest.psl
  • 1.1 lines changed: 5, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/basicListTest.rna.fa
  • 1.1 lines changed: 134, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.gp
  • 1.1 lines changed: 3, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.meta
  • 1.2 lines changed: 3, context: html, text, full: html, text
    added CDS to meta data
  • 1.1 lines changed: 4, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.prot.fa
  • 1.1 lines changed: 17, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.psl
  • 1.1 lines changed: 3, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.rna.fa
  • 1.1 lines changed: 72, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/input/basic.acc
  • 1.1 lines changed: 5, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/input/versioned.acc
  • 1.1 lines changed: 3, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/inc/maf.h
  • 1.30 lines changed: 5, context: html, text, full: html, text
    added option to filter mafs by species prefix
• src/lib/maf.c
  • 1.41 lines changed: 21, context: html, text, full: html, text
    added option to filter mafs by species prefix
• src/parasol/paraHub/paraHub.c
  • 1.132 lines changed: 9, context: html, text, full: html, text
    fixed incorrect usage message
• src/parasol/paraNode/paraNode.c
  • 1.82 lines changed: 24, context: html, text, full: html, text
    added option to allow setting arbitrary environment variable for jobs
• src/parasol/paraNodeStart/paraNodeStart.c
  • 1.15 lines changed: 12, context: html, text, full: html, text
    added option to allow setting arbitrary environment variable for jobs
• src/parasol/parasol/parasol.c
  • 1.48 lines changed: 7, context: html, text, full: html, text
    added an option to connect to a remote hub (for jobTree)