hiram: changes by file

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

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