hiram: changes by commit

review to branch (2009-06-30 to 2009-07-07) v210

• Rerun all the equCab2 chains and nets to clean up problems
  • src/hg/makeDb/doc/canFam2.txt 1.20 - lines changed: 123, context: html, text, full: html, text
  • src/hg/makeDb/doc/equCab2.txt 1.26 - lines changed: 141, context: html, text, full: html, text
  • src/hg/makeDb/doc/galGal3.txt 1.28 - lines changed: 51, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg18.txt 1.367 - lines changed: 57, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm9.txt 1.101 - lines changed: 54, context: html, text, full: html, text
  • src/hg/makeDb/doc/monDom5.txt 1.11 - lines changed: 63, context: html, text, full: html, text
  • src/hg/makeDb/doc/ornAna1.txt 1.25 - lines changed: 18, context: html, text, full: html, text
• Making upstream maf files from the 7-way alignment
  • src/hg/makeDb/doc/sacCer2.txt 1.10 - lines changed: 27, context: html, text, full: html, text
• Adding Horse chains and nets as a composite
  • src/hg/makeDb/trackDb/chainNet.html 1.1 - lines changed: 155, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.516 - lines changed: 39, context: html, text, full: html, text
• overrides for humanChainNet and horseChainNet
  • src/hg/makeDb/trackDb/opossum/trackDb.ra 1.29 - lines changed: 10, context: html, text, full: html, text
• Overrides for humanChainNet and horseChainNet
  • src/hg/makeDb/trackDb/platypus/trackDb.ra 1.3 - lines changed: 6, context: html, text, full: html, text
• Fixup equCab2 chain net priorities and overrides for hg19 chain net composite
  • src/hg/makeDb/trackDb/dog/priority.ra 1.6 - lines changed: 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/trackDb.ra 1.22 - lines changed: 6, context: html, text, full: html, text
• horse and human chainNet overrides
  • src/hg/makeDb/trackDb/mouse/priority.ra 1.11 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.154 - lines changed: 10, context: html, text, full: html, text
• priority for human and horse chainNet composites
  • src/hg/makeDb/trackDb/chicken/priority.ra 1.8 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/trackDb.ra 1.10 - lines changed: 4, context: html, text, full: html, text
• No longer need the priority here, it is in the trackDb.ra now
  • src/hg/makeDb/trackDb/platypus/priority.ra 1.2 - lines changed: 7, context: html, text, full: html, text
• Composite chain/net tracks for equCab2 release, chicken, platypus, opossum, human, mouse, dog
  • src/hg/makeDb/trackDb/trackDb.ra 1.517 - lines changed: 211, context: html, text, full: html, text
• EquCab2 track moved up to the composite
  • src/hg/makeDb/trackDb/chicken/trackDb.ra 1.11 - lines changed: 14, context: html, text, full: html, text
• Needs SOCKETLIB for build on Solaris
  • src/index/bptLookupStringToBits64/makefile 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/index/bptMakeStringToBits64/makefile 1.3 - lines changed: 1, context: html, text, full: html, text
• Needs SOCKETLIB for build on solaris
  • src/index/bptForTwoBit/makefile 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/weblet/bottleneck/makefile 1.8 - lines changed: 1, context: html, text, full: html, text
• dding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
  • src/utils/bedToBigBed/makefile 1.5 - lines changed: 14, context: html, text, full: html, text
  • src/utils/bigBedSummary/makefile 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/makefile 1.72 - lines changed: 1, context: html, text, full: html, text
• adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
  • src/utils/bigBedToBed/makefile 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/bigWigSummary/makefile 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/bigWigToBedGraph/makefile 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/faToTwoBit/makefile 1.14 - lines changed: 1, context: html, text, full: html, text
  • src/utils/findMotif/makefile 1.8 - lines changed: 1, context: html, text, full: html, text
  • src/utils/pslToPslx/makefile 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/utils/twoBitInfo/makefile 1.9 - lines changed: 1, context: html, text, full: html, text
  • src/utils/twoBitToFa/makefile 1.14 - lines changed: 1, context: html, text, full: html, text
  • src/utils/udcCleanup/makefile 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/makefile 1.6 - lines changed: 1, context: html, text, full: html, text
• Fixing a gap confusion bug
  • src/utils/findMotif/findMotif.c 1.13 - lines changed: 6, context: html, text, full: html, text