hiram: changes by commit

branch to review (2010-03-02 to 2010-03-16) v227

• replace tetNig1 with tetNig2 in vertebrate chainNet
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.100 - lines changed: 6, context: html, text, full: html, text
• replace tetNig1 with tetNig2 chainNet
  • src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra 1.2 - lines changed: 1, context: html, text, full: html, text
• find defaultGenome from hg.conf if present
  • src/hg/lib/hdb.c 1.420 - lines changed: 3, context: html, text, full: html, text
• add defaultGenome variable discussion, pointer to README.udc and fixup comments for downloadsServer
  • src/product/ex.hg.conf 1.22 - lines changed: 19, context: html, text, full: html, text
• adding 13-way definition
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra 1.3 - lines changed: 37, context: html, text, full: html, text
• fix semiUniqName when host name includes : as in: localhost:8080 (from 41,000 ft)
  • src/lib/osunix.c 1.46 - lines changed: 1, context: html, text, full: html, text
• need to clean in g2cCheck
  • src/cdnaAli/makefile 1.5 - lines changed: 3, context: html, text, full: html, text
• need to clean hgTomRough
  • src/hg/makeDb/makefile 1.45 - lines changed: 3, context: html, text, full: html, text
• need to clean algo.msg for clean target
  • src/hg/pslCDnaFilter/makefile 1.14 - lines changed: 1, context: html, text, full: html, text
• needed a clean target
  • src/hg/pslPartition/makefile 1.6 - lines changed: 3, context: html, text, full: html, text
• add clean target and use curly braces on variables
  • src/hg/snp/makefile 1.4 - lines changed: 6, context: html, text, full: html, text
• need a clean target
  • src/isPcr/makefile 1.2 - lines changed: 5, context: html, text, full: html, text
  • src/xenoAli/dynAlign/makefile 1.9 - lines changed: 3, context: html, text, full: html, text
• need clean targets everywhere here
  • src/xenoAli/bwana/makefile 1.8 - lines changed: 3, context: html, text, full: html, text
  • src/xenoAli/makefile 1.4 - lines changed: 5, context: html, text, full: html, text
  • src/xenoAli/stitcher/makefile 1.8 - lines changed: 3, context: html, text, full: html, text
• Well, we need a clean in simpleChain
  • src/hg/mouseStuff/makefile 1.23 - lines changed: 3, context: html, text, full: html, text