markd: changes by commit

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

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