File Changes for braney

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

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