File Changes for angie

v337_base to v338_preview (2016-08-15 to 2016-08-22) v338

• src/hg/checkHgFindSpec/checkHgFindSpec.c
  • lines changed 4, context: html, text, full: html, text
    b3fcbb7d6139a1993f5f02261ae3b495bc3edf41 Mon Aug 15 10:43:26 2016 -0700
    Increased verbosity level to 2 for no match & no table info lines.
    
• src/hg/checkTableCoords/checkTableCoords.c
  • lines changed 13, context: html, text, full: html, text
    53280f702308da193ac7565e25d29d571e06d3b7 Fri Aug 19 10:51:59 2016 -0700
    Added a check for bad chrom name for scaffold-based assemblies. All other checks are still skipped for scaffold-based assemblies! refs #17919
    
• src/hg/inc/hgHgvs.h
  • lines changed 74, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/hgFind.c
  • lines changed 60, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/hgHgvs.c
  • lines changed 531, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/tests/expected/hgvs/validTerms.txt
  • lines changed 11, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/tests/hgvsTester.c
  • lines changed 72, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/tests/hgvsTests.mk
  • lines changed 18, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/tests/input/hgvs/validTerms.txt
  • lines changed 16, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/inc/dnautil.h
  • lines changed 8, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/inc/regexHelper.h
  • lines changed 21, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/lib/dnautil.c
  • lines changed 33, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/lib/regexHelper.c
  • lines changed 44, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554