hiram: changes by commit

review to branch (2009-12-09 to 2009-12-14) v221

• backward autoScale default for custom tracks, have autoScale on by default
  • src/hg/lib/wiggleCart.c 1.36 - lines changed: 7, context: html, text, full: html, text
• unlink the custom wia file after it is open so it will disappear if the loader fails
  • src/hg/lib/customFactory.c 1.113 - lines changed: 3, context: html, text, full: html, text
• Fixup central.domain and central.cookie comments
  • src/product/ex.hg.conf 1.20 - lines changed: 8, context: html, text, full: html, text
• Indicate the loading procedure for a bigWig file.
  • src/hg/makeDb/trackDb/README 1.95 - lines changed: 9, context: html, text, full: html, text
• No need to mention the cookie
  • src/product/ex.hg.conf 1.21 - lines changed: 5, context: html, text, full: html, text
• Eliminate much of the garbage from other chain tables and find appropriate tree in the phylo tree
  • src/hg/utils/phyloTrees/chainNet.pl 1.3 - lines changed: 53, context: html, text, full: html, text
• no need to have bosTau2.chainNet here
  • src/hg/makeDb/trackDb/human/hg17/bosTau2.chainNet.html 1.2 - lines changed: 153, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm7/bosTau2.chainNet.html 1.2 - lines changed: 153, context: html, text, full: html, text
• fixup chainNet priorities for bosTau2
  • src/hg/makeDb/trackDb/chainBosTau2.html 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.chainNet.ra 1.1 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.478 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/chainBosTau2.html 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra 1.1 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.165 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.4 - lines changed: 42, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.550 - lines changed: 32, context: html, text, full: html, text
• add chainMinScore to the bosTau2 chain entries
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.166 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.551 - lines changed: 1, context: html, text, full: html, text
• Needed some release alpha tags to avoid errors
  • src/hg/makeDb/trackDb/worm/trackDb.ra 1.39 - lines changed: 6, context: html, text, full: html, text
• Check chain.csh file in lastz/blastz run for parameters
  • src/hg/utils/phyloTrees/findScores.pl 1.1 - lines changed: 67, context: html, text, full: html, text
• bosTau3 is now ready for chainNet composite
  • src/hg/makeDb/trackDb/human/trackDb.chainNet.ra 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra 1.2 - lines changed: 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.167 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra 1.1 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.5 - lines changed: 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.552 - lines changed: 5, context: html, text, full: html, text
• bosTau4 chain and net is now ready for composite
  • src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra 1.1 - lines changed: 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.chainNet.ra 1.3 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra 1.3 - lines changed: 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra 1.1 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.6 - lines changed: 42, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.553 - lines changed: 5, context: html, text, full: html, text
• felCat3 chain and nets are now composites
  • src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra 1.2 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.chainNet.ra 1.4 - lines changed: 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra 1.4 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.7 - lines changed: 58, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.554 - lines changed: 6, context: html, text, full: html, text