File Changes for angie

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

src/hg/hgTables/hgTables.h
- lines changed 3, 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/intersect.c
- lines changed 3, 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/mainPage.c
- lines changed 1, 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/inc/customPp.h
- lines changed 3, context: html, text, full: html, text
  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/lib/customFactory.c
- lines changed 161, context: html, text, full: html, text
  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/lib/customPp.c
- lines changed 9, context: html, text, full: html, text
  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/lib/customTrack.c
- lines changed 42, context: html, text, full: html, text
  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/lib/gpFx.c
- lines changed 4, context: html, text, full: html, text
  Fixed coord-arithmetic bug that caused crash for user in MLQ #12778.refs #12778
src/hg/lib/trackHub.c
- lines changed 6, context: html, text, full: html, text
  Use vcfTabixFileMayOpen instead of vcfFileMayOpen so that we alsocheck the tabix index file.
src/hg/makeDb/doc/bosTau7.txt
- lines changed 12, 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/canFam3.txt
- lines changed 11, 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/galGal4.txt
- lines changed 15, 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/susScr3.txt
- lines changed 13, 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/utils/automation/collectNcbiFuncAnnotations.pl
- lines changed 3, 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/inc/linefile.h
- lines changed 2, context: html, text, full: html, text
  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/lib/linefile.c
- lines changed 1, context: html, text, full: html, text
  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

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