File Changes for hiram

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

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