Commits for angie

v291_preview to v291_preview2 (2013-10-07 to 2013-10-14) v291

• Fix for the latest bug uncovered by the tenacious users of MLQ #11775:a deletion that spans the UTR/CDS boundary was something I hadn't tested
  against yet.
  refs #11775
  
  • src/hg/lib/gpFx.c - lines changed 12, context: html, text, full: html, text
• Updating links to Galaxy. refs #11898
  • src/hg/hgTables/galaxy.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTables/usage.c - lines changed 1, context: html, text, full: html, text
• Fixing unsigned int underflow (affects variants in first 5000 bases of chrom).
  • src/hg/lib/annoGratorGpVar.c - lines changed 4, context: html, text, full: html, text
• Don't add splice_region_variant for a variant that falls at beginningor end of transcript -- only for actual splice regions.
  
  • src/hg/lib/gpFx.c - lines changed 4, context: html, text, full: html, text
• Found one more place where a resetMergeState was necessary.Without the reset, large-bin items from the previous chrom could
  still be hanging out in bigItemQueue when we query the next chrom.
  
  • src/hg/lib/annoStreamDb.c - lines changed 3, context: html, text, full: html, text
• qTail->start should be compared to region end only when it's on the same chrom.
  • src/lib/annoGrator.c - lines changed 2, context: html, text, full: html, text
• Calling asdDoQueryChunking from way down in nextRowFromBuffer wasn'ta good idea because nextRowFromBuffer might have a caller that assumes
  we're done merging... but after calling asdDoQueryChunking, we need
  to start over with the merging. So, return NULL, but set self->needQuery;
  then, way up in asdNextRow, if we get a NULL, then check self->needQuery,
  and try again if necessary.
  
  • src/hg/lib/annoStreamDb.c - lines changed 24, context: html, text, full: html, text