Commits for angie

v283_preview to v283_preview2 (2013-04-23 to 2013-04-30) v283

• Added determination of data type by asObject comparison instead ofkludges like special annoRowType or checking a few column names. refs #6152
  
  • src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 1, context: html, text, full: html, text
• Making annoGratorGpVar able to handle VCF input too. In order for a grator tosee what type of input is coming from the primary source, the streamer should
  be passed in along with the primary row, as it is for formatters now.
  refs #6152
  
  • src/hg/inc/annoGratorGpVar.h - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/variant.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/annoFormatVep.c - lines changed 32, context: html, text, full: html, text
  • src/hg/lib/annoGratorGpVar.c - lines changed 44, context: html, text, full: html, text
  • src/hg/lib/variant.c - lines changed 20, context: html, text, full: html, text
  • src/inc/annoFormatter.h - lines changed 12, context: html, text, full: html, text
  • src/inc/annoGrator.h - lines changed 2, context: html, text, full: html, text
  • src/inc/annoStreamer.h - lines changed 14, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 4, context: html, text, full: html, text
  • src/lib/annoFormatter.c - lines changed 13, context: html, text, full: html, text
  • src/lib/annoGrateWig.c - lines changed 3, context: html, text, full: html, text
  • src/lib/annoGrator.c - lines changed 2, context: html, text, full: html, text
  • src/lib/annoGratorQuery.c - lines changed 1, context: html, text, full: html, text
  • src/lib/annoStreamer.c - lines changed 15, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 23, context: html, text, full: html, text
• typo fix in comment
  • src/hg/inc/variant.h - lines changed 2, context: html, text, full: html, text
• Adding NULL check.
  • src/hg/lib/tests/annoGratorTester.c - lines changed 2, context: html, text, full: html, text
• Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
  stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
  represent insertion positions the way they do.
  TODO: lots more testing! and convert gpFx to use localmem.
  refs #6152
  
  • src/hg/inc/gpFx.h - lines changed 40, context: html, text, full: html, text
  • src/hg/inc/soTerm.h - lines changed 42, context: html, text, full: html, text
  • src/hg/lib/annoFormatVep.c - lines changed 53, context: html, text, full: html, text
  • src/hg/lib/annoGratorGpVar.c - lines changed 116, context: html, text, full: html, text
  • src/hg/lib/gpFx.c - lines changed 284, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt - lines changed 49, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 12, context: html, text, full: html, text
• Converted variant and gpFx to use localmem. Also got rid of a coupleunnecessary conversions from genePred to bed and psl in annoGratorGpVar
  and gpFx. refs #6152
  
  • src/hg/inc/gpFx.h - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/variant.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/annoGratorGpVar.c - lines changed 48, context: html, text, full: html, text
  • src/hg/lib/gpFx.c - lines changed 197, context: html, text, full: html, text
  • src/hg/lib/variant.c - lines changed 12, context: html, text, full: html, text
  • src/inc/localmem.h - lines changed 3, context: html, text, full: html, text
• Code review feedback, thanks Tim. refs #10680
  • src/hg/lib/annoFormatVep.c - lines changed 2, context: html, text, full: html, text
  • src/inc/annoStreamer.h - lines changed 1, context: html, text, full: html, text