hiram: changes by commit

review to branch (2009-06-16 to 2009-06-23) v209

• Turning on first look at 46-way alignment
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.31 - lines changed: 170, context: html, text, full: html, text
• Adding an itemRgb test example
  • src/utils/bedToBigBed/itemRgb.as 1.1 - lines changed: 13, context: html, text, full: html, text
  • src/utils/bedToBigBed/itemRgb.bed 1.1 - lines changed: 21, context: html, text, full: html, text
• The spaces need to be tabs since that is what comes out of bigBedToBed
  • src/utils/bedToBigBed/itemRgb.bed 1.2 - lines changed: 0, context: html, text, full: html, text
• Fixup background color on Links Out table when only one row of links ...
  • src/hg/hgGene/links.c 1.38 - lines changed: 0, context: html, text, full: html, text
• Beginning to work through this script to get it ready for UCSC gene build
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes11.csh 1.1 - lines changed: 1121, context: html, text, full: html, text
• Cytobands done, Venter Poodle chain/net done, starting 46-way conservation, exoniphy lifted from hg18, liftOver to hg18 done.
  • src/hg/makeDb/doc/hg19.txt 1.26 - lines changed: 695, context: html, text, full: html, text
• Need to load exoniphy manually, it seems to have different columns in it ?
  • src/hg/makeDb/doc/hg19.txt 1.27 - lines changed: 8, context: html, text, full: html, text
• Have proceeded through the first cluster job OK without CCDS genes
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes11.csh 1.2 - lines changed: 28, context: html, text, full: html, text
• bedSplitOnChrom should be on the build list, used in UCSC gene production
  • src/hg/makefile 1.152 - lines changed: 1, context: html, text, full: html, text