Commits for angie

v296_base to v297_preview (2014-02-24 to 2014-03-03) v297

• Improved error messages for bigData custom track common mistakes likemissing bigDataUrl setting or trying to upload a bigData file instead
  of making a track line with a public URL. I added a new "factory"
  to customFactory.c that produces no tracks, only error messages about
  directly uploaded bigData files.
  refs #12747
  
  • src/hg/inc/customPp.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/customFactory.c - lines changed 161, context: html, text, full: html, text
  • src/hg/lib/customPp.c - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/customTrack.c - lines changed 42, context: html, text, full: html, text
  • src/inc/linefile.h - lines changed 2, context: html, text, full: html, text
  • src/lib/linefile.c - lines changed 1, context: html, text, full: html, text
• Use vcfTabixFileMayOpen instead of vcfFileMayOpen so that we alsocheck the tabix index file.
  
  • src/hg/lib/trackHub.c - lines changed 6, context: html, text, full: html, text
• Fixing a couple bugs uncovered by MLQ #12777: first, the intersectionbutton was appearing even for tables that don't pass canIntersect().
  Second, canIntersect() was returning false for VCF instead of true.
  So the intersect button appeared for VCF tracks, but the user's
  intersection settings were ignored. Now intersection works for VCF.
  refs #12777
  
  • src/hg/hgTables/hgTables.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTables/intersect.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c - lines changed 1, context: html, text, full: html, text
• Brian L found that hgc crashed on snp138 in cow & pig. That wascaused by invalid table contents due to a bug in the script
  collectNcbiFuncAnnotations.pl. Fixed the bug, removed a bogus
  warning, and re-ran the script for cow, pig, chicken and dog.
  refs #12490
  
  • src/hg/makeDb/doc/bosTau7.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/canFam3.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/galGal4.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/susScr3.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/utils/automation/collectNcbiFuncAnnotations.pl - lines changed 3, context: html, text, full: html, text
• Fixed coord-arithmetic bug that caused crash for user in MLQ #12778.refs #12778
  
  • src/hg/lib/gpFx.c - lines changed 4, context: html, text, full: html, text