Commits for braney

v261_preview2 to v261_base (2011-12-20 to 2012-01-03) v261

• tests for the new functions of pslCDnaFilter, and a fix to blackList.c that I discovered when creating the tests ;-)
  • src/hg/pslCDnaFilter/tests/expected/blackListTest/filt.out - lines changed 6, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/blackListTest/keep.psl - lines changed 397, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/decayMinCoverTest/filt.out - lines changed 6, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/decayMinCoverTest/keep.psl - lines changed 84, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/input/blackList.psl - lines changed 478, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/input/blackList.txt - lines changed 3, context: html, text, full: html, text
  • src/lib/blackList.c - lines changed 4, context: html, text, full: html, text
• oops... need the makefile for the tests
  • src/hg/pslCDnaFilter/tests/makefile - lines changed 7, context: html, text, full: html, text
• added some more interesting psl's to the decayMinCoverTest
  • src/hg/pslCDnaFilter/tests/expected/decayMinCoverTest/filt.out - lines changed 3, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/decayMinCoverTest/keep.psl - lines changed 50, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/input/decayMinCover.psl - lines changed 573, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/makefile - lines changed 1, context: html, text, full: html, text
• drop inactive assemblies #6358
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 458, context: html, text, full: html, text
• resolve merge conflict
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text
• drop the unused assemblies #6358
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 12, context: html, text, full: html, text
• purge assemblies from active align list #6358. Also add back hg15test to genbank.conf per Mark
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 12, context: html, text, full: html, text
• oops, had some truncated lines in last checkin #6358
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 5, context: html, text, full: html, text
• follow more consistent rules about which assemblies fall into which class (low-coverage, well-ordered, finished) #6250
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 221, context: html, text, full: html, text
• oops, typo... lowcover should be lowCover (#6250)
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 94, context: html, text, full: html, text
• add an mRNA that changed from pig to panda. Simple mistake, eh?
  • src/hg/makeDb/genbank/etc/ignore.idx - lines changed 1, context: html, text, full: html, text
• v261 final build
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• New version number v261
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text