hiram: changes by file

branch to review (2009-12-01 to 2009-12-09) v221

• src/hg/featureBits/featureBits.c
  • 1.57 lines changed: 2, context: html, text, full: html, text
    Fix usage message for chromSize argument
  • 1.56 lines changed: 3, context: html, text, full: html, text
    Really do not contact the database unless it is actually required
• src/hg/hgTracks/hgTracks.c
  • 1.1610 lines changed: 3, context: html, text, full: html, text
    Add lowetooltip.js inclusion on behalf of Andrew Holmes
• src/hg/makeDb/doc/hg19.txt
  • 1.66 lines changed: 39, context: html, text, full: html, text
    Final loaded phastCons and phyloP for 46-way alignment
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.3 lines changed: 162, context: html, text, full: html, text
    All chain net tracks in Marmoset are now composite tracks
  • 1.2 lines changed: 82, context: html, text, full: html, text
    adding chainNetRn4 and chainNetHg18 for Cow bosTau browsers and setting appropriate release tags to separate from older individual tracks
  • 1.1 lines changed: 559, context: html, text, full: html, text
    Move all the chainNet definitions off to their own file
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.549 lines changed: 8, context: html, text, full: html, text
    All chain net tracks in Marmoset are now composite tracks
  • 1.548 lines changed: 8, context: html, text, full: html, text
    adding chainNetRn4 and chainNetHg18 for Cow bosTau browsers and setting appropriate release tags to separate from older individual tracks
  • 1.547 lines changed: 561, context: html, text, full: html, text
    Move all the chainNet definitions off to their own file
  • 1.544 lines changed: 2, context: html, text, full: html, text
    fixup duplicate chainCalJac1 and chainPanTro2 entries
• src/hg/makeDb/trackDb/chicken/trackDb.ra
  • 1.12 lines changed: 8, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/cow/trackDb.chainNet.ra
  • 1.1 lines changed: 25, context: html, text, full: html, text
    all chains and nets on any Cow browser are now composites
• src/hg/makeDb/trackDb/cow/trackDb.ra
  • 1.4 lines changed: 7, context: html, text, full: html, text
    all chains and nets on any Cow browser are now composites
• src/hg/makeDb/trackDb/cow/bosTau2/trackDb.ra
  • 1.8 lines changed: 2, context: html, text, full: html, text
    all chains and nets on any Cow browser are now composites
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.18 lines changed: 8, context: html, text, full: html, text
    all chains and nets on any Cow browser are now composites
• src/hg/makeDb/trackDb/dog/trackDb.ra
  • 1.25 lines changed: 6, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
  • 1.24 lines changed: 15, context: html, text, full: html, text
    fixup duplicate chainCalJac1 and chainPanTro2 entries
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.39 lines changed: 25, context: html, text, full: html, text
    fixup duplicate chainCalJac1 and chainPanTro2 entries
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.60 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra
  • 1.7 lines changed: 32, context: html, text, full: html, text
    Eliminate duplicate definitions of chainHg18 and chainMm9 they are already overridden here
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • 1.576 lines changed: 1, context: html, text, full: html, text
    Eliminate duplicate spanList definition
• src/hg/makeDb/trackDb/human/hg17/bosTau2.chainNet.html
  • 1.1 lines changed: 153, context: html, text, full: html, text
    Ancient chain and net has no axtChain command.
• src/hg/makeDb/trackDb/human/hg17/trackDb.encode.ra
  • 1.178 lines changed: 1, context: html, text, full: html, text
    eliminate a duplicate maxHeightPixels definition
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.699 lines changed: 1, context: html, text, full: html, text
    set autoscale to properly read autoscale
• src/hg/makeDb/trackDb/lamprey/trackDb.ra
  • 1.5 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/lizard/trackDb.ra
  • 1.5 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
  • 1.2 lines changed: 25, context: html, text, full: html, text
    In same order as conservation track
  • 1.1 lines changed: 39, context: html, text, full: html, text
    All chain net tracks in Marmoset are now composite tracks
• src/hg/makeDb/trackDb/marmoset/trackDb.ra
  • 1.6 lines changed: 11, context: html, text, full: html, text
    All chain net tracks in Marmoset are now composite tracks
• src/hg/makeDb/trackDb/medaka/trackDb.ra
  • 1.16 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.161 lines changed: 6, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
  • 1.160 lines changed: 9, context: html, text, full: html, text
    Eliminate duplicate xenoRefGene entry
• src/hg/makeDb/trackDb/mouse/mm7/bosTau2.chainNet.html
  • 1.1 lines changed: 153, context: html, text, full: html, text
    Ancient chain track has no axtChain
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.59 lines changed: 25, context: html, text, full: html, text
    fix autoscale to read properly autoScale
• src/hg/makeDb/trackDb/opossum/trackDb.ra
  • 1.33 lines changed: 11, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/platypus/trackDb.ra
  • 1.5 lines changed: 10, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/rabbit/ctgPos2.html
  • 1.1 lines changed: 8, context: html, text, full: html, text
    Adding ctgPos2 track for oryCun2
• src/hg/makeDb/trackDb/rabbit/trackDb.ra
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Adding ctgPos2 track for oryCun2
• src/hg/makeDb/trackDb/rat/rn5/trackDb.ra
  • 1.2 lines changed: 47, context: html, text, full: html, text
    Obsolete genome at this time. May reappear sometime in the future
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.49 lines changed: 10, context: html, text, full: html, text
    eliminate duplicate entry for phastConsElements5way
• src/hg/makeDb/trackDb/shrew/sorAra1/description.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding link to sequencing center project page
• src/hg/makeDb/trackDb/squirt/ci1/trackDb.ra
  • 1.51 lines changed: 11, context: html, text, full: html, text
    Eliminate duplicate entry for blastzOikDio0
  • 1.50 lines changed: 1, context: html, text, full: html, text
    Eliminate a stray track definition line for blastzCioSav1
• src/hg/makeDb/trackDb/squirt/ci2/trackDb.ra
  • 1.8 lines changed: 12, context: html, text, full: html, text
    eliminate duplicate entries for blastzCioSav1 and blastzOikDio0
• src/hg/makeDb/trackDb/squirt/cioSav2/trackDb.ra
  • 1.7 lines changed: 12, context: html, text, full: html, text
    eliminate duplicate entries for blastzCioSav1 and blastzOikDio0
• src/hg/makeDb/trackDb/stickleback/trackDb.ra
  • 1.19 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
  • 1.40 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/worm/ce2/trackDb.ra
  • 1.36 lines changed: 11, context: html, text, full: html, text
    eliminate duplicate definition for axtNetCb1
• src/hg/makeDb/trackDb/worm/ce6/trackDb.ra
  • 1.16 lines changed: 42, context: html, text, full: html, text
    Some Fire Lab experiments
• src/hg/makeDb/trackDb/worm/ce7/trackDb.ra
  • 1.5 lines changed: 3, context: html, text, full: html, text
    ensGene default pack
• src/hg/makeDb/trackDb/xenTro/trackDb.ra
  • 1.21 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/zebraFinch/trackDb.ra
  • 1.4 lines changed: 5, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.55 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/utils/phyloTrees/46way.dissect.txt
  • 1.1 lines changed: 637, context: html, text, full: html, text
    Initial contents
• src/hg/utils/phyloTrees/46way.nh
  • 1.1 lines changed: 21, context: html, text, full: html, text
    Initial contents
• src/hg/utils/phyloTrees/chainNet.pl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Eliminate confusion from chainSelf tracks
  • 1.1 lines changed: 77, context: html, text, full: html, text
    Initial source appears to work OK
• src/hg/utils/phyloTrees/rerootTree.pl
  • 1.1 lines changed: 104, context: html, text, full: html, text
    Initial contents