Commits for braney

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

• a little fix from greg
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text
• added decay model option to calculate minimum coverage based on query size (#20)
  • src/hg/pslCDnaFilter/algo.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/pslCDnaFilter.c - lines changed 37, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/usage.txt - lines changed 5, context: html, text, full: html, text
• take out release alpha on parent for merck track (for Fan)
  • src/hg/makeDb/trackDb/human/hg19/trackDb.merckPolyA.all.ra - lines changed 1, context: html, text, full: html, text
• another tweak, stepSize=5 only on native mrna (#20)
  • src/hg/makeDb/genbank/src/align/gbBlat - lines changed 2, context: html, text, full: html, text
• oops, missed a few edits. Thanks Angie (#6212)
  • src/hg/zoo/zooLib/args.c - lines changed 4, context: html, text, full: html, text
  • src/hg/zoo/zooLib/util.c - lines changed 2, context: html, text, full: html, text
• fix comment. Thanks Angie! (#6212)
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text
• fix a problem with disconnecting a hub, followed by using the blue bar to navigate away (#6273)
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 4, context: html, text, full: html, text
• 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/genbank/src/dbload/gbLoadRna.c - lines changed 6, context: html, text, full: html, text
• 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/etc/genbank.conf - lines changed 1, context: html, text, full: html, text