Commits for braney

v285_preview to v285_preview2 (2013-06-04 to 2013-06-11) v285

• ongoing work on UCSC genes for hg19
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh - lines changed 146, context: html, text, full: html, text
• change TreeFam link out URL refs #10874
  • src/hg/hgGene/hgGeneData/links.ra - lines changed 1, context: html, text, full: html, text
• increase the size of buffer that was being exceeded on SOD1
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text
• make title field 1024 instead of 255 because it was getting truncated.
  • src/hg/lib/gwasCatalog.sql - lines changed 1, context: html, text, full: html, text
• first pass at documentation for assembly hubs and track item search refs #8072
  • src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html - lines changed 90, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html - lines changed 6, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 22, context: html, text, full: html, text
• add new html files for trix and twoBit.
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trix.html - lines changed 45, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/twoBit.html - lines changed 58, context: html, text, full: html, text
• clean up twoBit and trix pages a bit. Still need a lot of work
  • src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trix.html - lines changed 13, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/twoBit.html - lines changed 26, context: html, text, full: html, text
• notify folks that genome graphs doesn't work with assembly hubs
  • src/hg/hgGenome/hgGenome.c - lines changed 3, context: html, text, full: html, text
• add most current reactome tables to proteome database
  • src/hg/makeDb/doc/proteins/121210.txt - lines changed 9, context: html, text, full: html, text
• clean up some TODO's in UCSC genes, add some notes for next time, fix txCdsToGene to continue after a warning.
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh - lines changed 23, context: html, text, full: html, text
  • src/hg/txCds/txCdsToGene/txCdsToGene.c - lines changed 3, context: html, text, full: html, text
• fill in browserName for hgPos records so hgFind will highlight the element refs #10426
  • src/hg/lib/trackHub.c - lines changed 1, context: html, text, full: html, text
• add kg6ToKg7 for UCSC genes
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text