Commits for hiram

v256_preview to v256_preview2 (2011-08-16 to 2011-08-23) v256

• initial contents to transform infoOut.txt to ensemblToGeneName.tab reference
  • src/hg/utils/automation/ensemblToGeneName.pl - lines changed 52, context: html, text, full: html, text
• adding ensemblToGeneName.pl to the scripts list
  • src/hg/utils/automation/makefile - lines changed 1, context: html, text, full: html, text
• now showing geneName from ensemblToGeneName table for ensGene items
  • src/hg/hgc/hgc.c - lines changed 23, context: html, text, full: html, text
• add in the business to create the ensemblToGeneName translation table
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 6, context: html, text, full: html, text
• now showing correctly protein coding vs not for Ensembl genes
  • src/hg/hgc/hgc.c - lines changed 31, context: html, text, full: html, text
• now adding ensemblSource table for coding status
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensemblInfo.pl - lines changed 62, context: html, text, full: html, text
• ensemblToGeneName becomes the generic ensemblInfo
  • src/hg/utils/automation/makefile - lines changed 1, context: html, text, full: html, text
• has become the generic ensemblInfo.pl
  • src/hg/utils/automation/ensemblToGeneName.pl - lines changed 52, context: html, text, full: html, text
• correct casing on title
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text
• adding ensemblToGeneName and ensemblSource tables to ensGene checks and all assemblies that have ensGene
  • src/hg/makeDb/schema/all.joiner - lines changed 24, context: html, text, full: html, text
• proper list of wgs assemblies and all new Ensembl gene definitions
  • src/hg/makeDb/schema/all.joiner - lines changed 34, context: html, text, full: html, text
• add the susScr2 lift from susScr1
  • src/hg/makeDb/doc/makeEnsembl.txt - lines changed 43, context: html, text, full: html, text
• moving deCODE Recomb up one level to get both hg18 and hg19 in one definition
  • src/hg/makeDb/trackDb/human/decode.rmap.ra - lines changed 165, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/decodeRmap.html - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/decode.rmap.ra - lines changed 164, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/decodeRmap.html - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text
• adjust color for female track
  • src/hg/makeDb/trackDb/human/decode.rmap.ra - lines changed 1, context: html, text, full: html, text
• add pennantIcon for hg18 to decodeRmap
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 3, context: html, text, full: html, text
• add the deCODE recomb lift over track from hg18
  • src/hg/makeDb/doc/hg19.txt - lines changed 81, context: html, text, full: html, text
• adding susScr2 for ensGene
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• added cpgIsland track per user request
  • src/hg/makeDb/doc/anoCar2.txt - lines changed 84, context: html, text, full: html, text