File Changes for braney

v260_base to v261_preview (2011-12-06 to 2011-12-13) v261

• src/hg/hgHubConnect/hgHubConnect.c
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    a little fix from greg
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    fix comment. Thanks Angie! (#6212)
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    fix a problem with disconnecting a hub, followed by using the blue bar to navigate away (#6273)
• src/hg/makeDb/genbank/etc/genbank.conf
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    use new coverage rule for native mRNA on finished assemblys that takes into account the length of the query sequence using a linear function that requires more coverage the shorter the mRNA is. Related to #20.
• src/hg/makeDb/genbank/src/align/gbBlat
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    another tweak, stepSize=5 only on native mrna (#20)
• src/hg/makeDb/genbank/src/dbload/gbLoadRna.c
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    increase SQL wait_timeout to 24 hours. Default of 8 hours wasn't long enough to load all of genbank on hg19. Related to #20
• src/hg/makeDb/trackDb/human/hg19/trackDb.merckPolyA.all.ra
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    take out release alpha on parent for merck track (for Fan)
• src/hg/pslCDnaFilter/algo.txt
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    added decay model option to calculate minimum coverage based on query size (#20)
• src/hg/pslCDnaFilter/pslCDnaFilter.c
  • lines changed 37, context: html, text, full: html, text
    added decay model option to calculate minimum coverage based on query size (#20)
• src/hg/pslCDnaFilter/usage.txt
  • lines changed 5, context: html, text, full: html, text
    added decay model option to calculate minimum coverage based on query size (#20)
• src/hg/zoo/zooLib/args.c
  • lines changed 4, context: html, text, full: html, text
    oops, missed a few edits. Thanks Angie (#6212)
• src/hg/zoo/zooLib/util.c
  • lines changed 2, context: html, text, full: html, text
    oops, missed a few edits. Thanks Angie (#6212)