Commits for angie

v326_base to v327_preview (2015-12-07 to 2015-12-14) v327

• Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
  Add hgVai options for adding in transcript status info: GENCODE tags
  when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
  refs #16502, #16503
  
  • src/hg/hgVai/hgVai.c - lines changed 366, context: html, text, full: html, text
  • src/hg/inc/annoFormatVep.h - lines changed 4, context: html, text, full: html, text
  • src/hg/inc/annoStreamDb.h - lines changed 5, context: html, text, full: html, text
  • src/hg/inc/jksql.h - lines changed 2, context: html, text, full: html, text
  • src/hg/js/hgVarAnnogrator.js - lines changed 23, context: html, text, full: html, text
  • src/hg/js/model/hgIntegrator/hgIntegratorModel.js - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/annoFormatVep.c - lines changed 101, context: html, text, full: html, text
  • src/hg/lib/annoStreamDb.c - lines changed 39, context: html, text, full: html, text
  • src/hg/lib/dbNsfpMutationTaster.as - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/dbNsfpSift.as - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/dbNsfpVest.as - lines changed 19, context: html, text, full: html, text
  • src/hg/lib/tests/annoGratorTester.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/variation.txt - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 105, context: html, text, full: html, text
  • src/hg/utils/dbNsfpToBed.pl - lines changed 157, context: html, text, full: html, text
• Corrected the description of knownCanonical for hg38 as suggested by Matt
  and fixed missing-geneSymbol bug found by Matt -- thanks!
  refs #16502
  
  • src/hg/hgVai/hgVai.c - lines changed 39, context: html, text, full: html, text
• Make "add pgSnp or VCF custom track" button go to the 'add custom tracks' page
  instead of the 'manage custom tracks' page -- but the "manage custom tracks" button
  still goes to the 'manage custom tracks' page.
  
  • src/hg/hgVai/hgVai.c - lines changed 3, context: html, text, full: html, text
  • src/hg/js/hgVarAnnogrator.js - lines changed 8, context: html, text, full: html, text
• Add 'add track hub' button next to 'add pgSnp or VCF custom track' button as
  suggested by Matt. Update dbNSFP v3 reference per Matt. Thanks!
  refs #16503, #16504
  
  • src/hg/hgVai/hgVai.c - lines changed 22, context: html, text, full: html, text
• Sequence Ontology name change: non_coding_exon_variant --> non_coding_transcript_exon_variant.
  
  • src/hg/lib/soTerm.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/gpFx.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/vepOutIndelTrim.txt - lines changed 4, context: html, text, full: html, text