Commits for angie

v302_preview to v302_preview2 (2014-06-16 to 2014-06-23) v302

• User suggestion - make lincRNAsTranscripts searchable.refs #13475
  
  • src/hg/makeDb/trackDb/human/hg19/lincRNAs.ra - lines changed 6, context: html, text, full: html, text
• hdb's hGetParent wasn't working because it used hMaybeTrackInfo whichlooks up only one track, not its parent or children. It was used in only
  one place in the code, so I replaced it with a call to tdbForTrack.
  fixes #13477 (Search results don't open super tracks)
  
  • src/hg/inc/hdb.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 22, context: html, text, full: html, text
  • src/hg/lib/hgFind.c - lines changed 17, context: html, text, full: html, text
• Removed semiShortCircuit behavior from stsMapAliasMrnaAcc becausesome aliases conflict with gene names, and if it triggers a short
  circuit then the user never sees the matches in gene & genbank tracks.
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 2, context: html, text, full: html, text
• Tweak to lincRNAsTranscripts search: all but one name in this trackare TCONS_* accessions that should short-circuit. The one anomalous
  name is a gene name and should not short-circuit, so it will go on
  to get matches in gene and genbank tracks.
  
  • src/hg/makeDb/trackDb/human/hg19/lincRNAs.ra - lines changed 2, context: html, text, full: html, text
• In asvSetRegion, don't try to set tabix region if chrom is NULL (position is genome)because that call will fail and then we'd get the wrong idea and set self->eof, oops.
  
  • src/lib/annoStreamVcf.c - lines changed 1, context: html, text, full: html, text