hiram: changes by commit

branch to review (2009-03-10 to 2009-03-17) v202

• Larger entry field for filter by chromosome on a chain track
  • src/hg/hgTrackUi/hgTrackUi.c 1.477 - lines changed: 1, context: html, text, full: html, text
• Haplotype chains and nets added
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.3 - lines changed: 157, context: html, text, full: html, text
• An attempt at a multi-view chain and net situation
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.4 - lines changed: 152, context: html, text, full: html, text
• added hg19.lift and hg19.hapRegions
  • src/hg/makeDb/genbank/etc/genbank.conf 1.330 - lines changed: 2, context: html, text, full: html, text
• incorrect path for hg19 unbridged lift file
  • src/hg/makeDb/genbank/etc/genbank.conf 1.331 - lines changed: 1, context: html, text, full: html, text
• Fixup chain and net trackUi so they will work in multi-views
  • src/hg/hgTrackUi/hgTrackUi.c 1.479 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/chainTrack.c 1.31 - lines changed: 9, context: html, text, full: html, text
  • src/hg/inc/chainCart.h 1.3 - lines changed: 3, context: html, text, full: html, text
  • src/hg/inc/hui.h 1.120 - lines changed: 3, context: html, text, full: html, text
  • src/hg/inc/trackDb.h 1.44 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/chainCart.c 1.2 - lines changed: 8, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.172 - lines changed: 30, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c 1.59 - lines changed: 7, context: html, text, full: html, text
• Fixup the haplotype multi-view
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.5 - lines changed: 65, context: html, text, full: html, text
• Going to try non-split tables for hg19
  • src/hg/makeDb/genbank/etc/genbank.conf 1.332 - lines changed: 1, context: html, text, full: html, text
• The haplotype mapping to reference is now bed 12
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.6 - lines changed: 3, context: html, text, full: html, text
• No need for chainColor setting
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.7 - lines changed: 1, context: html, text, full: html, text
• Added hg19 - Human - GRCh37
  • src/hg/makeDb/genbank/etc/align.dbs 1.95 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs 1.100 - lines changed: 1, context: html, text, full: html, text
• cpgIslands done, genbank run done, blatServers assigned
  • src/hg/makeDb/doc/hg19.txt 1.3 - lines changed: 150, context: html, text, full: html, text
• liftOver to hg19 done
  • src/hg/makeDb/doc/hg18.txt 1.358 - lines changed: 16, context: html, text, full: html, text
• Much more closer to a final description
  • src/hg/makeDb/trackDb/human/hg19/description.html 1.2 - lines changed: 183, context: html, text, full: html, text
• Updated descriptions to be close to final versions
  • src/hg/makeDb/trackDb/human/hg19/description.html 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/gap.html 1.2 - lines changed: 67, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/gold.html 1.2 - lines changed: 36, context: html, text, full: html, text
• eliminate the duplicate hiveDataGenomes specification, been fixed elsewhere
  • src/hg/utils/automation/HgAutomate.pm 1.24 - lines changed: 4, context: html, text, full: html, text
  • src/hg/utils/automation/doCpgIslands.pl 1.2 - lines changed: 6, context: html, text, full: html, text
  • src/hg/utils/automation/doWindowMasker.pl 1.8 - lines changed: 6, context: html, text, full: html, text
• New option -inclHap to pass along to the net stage, and properly find at least some kind of db name from the path
  • src/hg/utils/automation/doBlastzChainNet.pl 1.27 - lines changed: 17, context: html, text, full: html, text
• Fixup the naming of the chain track variables in the multi-view composite
  • src/hg/lib/hui.c 1.173 - lines changed: 6, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c 1.60 - lines changed: 1, context: html, text, full: html, text
• • src/hg/makeDb/trackDb/trackDb.ra 1.500 - lines changed: 22, context: html, text, full: html, text
• allow net tracks to color by gray scale, and fixing chain tracks Ui options
  • src/hg/hgTrackUi/hgTrackUi.c 1.480 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTracks/chainTrack.c 1.32 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTracks/netTrack.c 1.24 - lines changed: 41, context: html, text, full: html, text
  • src/hg/inc/hui.h 1.121 - lines changed: 22, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.176 - lines changed: 62, context: html, text, full: html, text
• Remember answers to hDbIsActive and hgDbExists, was being called thousands of times during a simple refresh
  • src/hg/lib/hdb.c 1.398 - lines changed: 24, context: html, text, full: html, text