File Changes for angie

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

• src/hg/hgVai/hgVai.c
  • lines changed 366, context: html, text, full: html, text
    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
    
  • lines changed 39, 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
    
  • lines changed 3, 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.
    
  • lines changed 22, 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/inc/annoFormatVep.h
  • lines changed 4, context: html, text, full: html, text
    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/inc/annoStreamDb.h
  • lines changed 5, context: html, text, full: html, text
    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/inc/jksql.h
  • lines changed 2, context: html, text, full: html, text
    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/js/hgVarAnnogrator.js
  • lines changed 23, context: html, text, full: html, text
    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
    
  • lines changed 8, 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/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 2, context: html, text, full: html, text
    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/lib/annoFormatVep.c
  • lines changed 101, context: html, text, full: html, text
    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/lib/annoStreamDb.c
  • lines changed 39, context: html, text, full: html, text
    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/lib/dbNsfpMutationTaster.as
  • lines changed 3, context: html, text, full: html, text
    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/lib/dbNsfpSift.as
  • lines changed 3, context: html, text, full: html, text
    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/lib/dbNsfpVest.as
  • lines changed 19, context: html, text, full: html, text
    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/lib/soTerm.c
  • lines changed 1, context: html, text, full: html, text
    Sequence Ontology name change: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 1, context: html, text, full: html, text
    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/lib/tests/expected/annoGrator/gpFx.txt
  • lines changed 1, context: html, text, full: html, text
    Sequence Ontology name change: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 2, context: html, text, full: html, text
    Sequence Ontology name change: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/lib/tests/expected/annoGrator/vepOutIndelTrim.txt
  • lines changed 4, context: html, text, full: html, text
    Sequence Ontology name change: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 64, context: html, text, full: html, text
    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/makeDb/schema/all.joiner
  • lines changed 105, context: html, text, full: html, text
    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/utils/dbNsfpToBed.pl
  • lines changed 157, context: html, text, full: html, text
    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