467f4d3064ca7f047614ce75ebc8eb48b156ae4d
angie
  Mon Dec 11 15:36:25 2017 -0800
Support NT_ and NW_ accessions in genomic HGVS terms (not just NC; some alts are NT/NW).

diff --git src/hg/lib/hgHgvs.c src/hg/lib/hgHgvs.c
index 0557301..fd6ad07 100644
--- src/hg/lib/hgHgvs.c
+++ src/hg/lib/hgHgvs.c
@@ -21,43 +21,43 @@
 if (pHgvs && *pHgvs)
     {
     struct hgvsVariant *hgvs = *pHgvs;
     freez(&hgvs->seqAcc);
     freez(&hgvs->seqGeneSymbol);
     freez(&hgvs->changes);
     freez(pHgvs);
     }
 }
 
 // Regular expressions for HGVS-recognized sequence accessions: LRG or versioned RefSeq:
 #define lrgTranscriptExp "(LRG_[0-9]+t[0-9]+)"
 #define lrgProteinExp "(LRG_[0-9]+p[0-9]+)"
 #define lrgRegionExp "(LRG_[0-9]+)"
 
-// NC = RefSeq reference assembly chromosome
+// NC = RefSeq reference assembly chromosome (NT = contig (e.g. alt), NW = patch)
 // NG = RefSeq incomplete genomic region (e.g. gene locus)
 // NM = RefSeq curated mRNA
 // NP = RefSeq curated protein
 // NR = RefSeq curated (non-coding) RNA
 #define geneSymbolExp "([A-Za-z0-9./_-]+)"
 #define optionalGeneSymbolExp "(\\(" geneSymbolExp "\\))?"
 #define versionedAccPrefixExp(p) "(" p "_[0-9]+(\\.[0-9]+)?)" optionalGeneSymbolExp
 //                                 ........................       accession and optional dot version
 //                                              ...........       optional dot version
 //                                                         ...... optional gene symbol in ()s
 //                                                          ....  optional gene symbol
-#define versionedRefSeqNCExp versionedAccPrefixExp("[NX]C")
+#define versionedRefSeqNCExp versionedAccPrefixExp("[NX][CTW]")
 #define versionedRefSeqNGExp versionedAccPrefixExp("[NX]G")
 #define versionedRefSeqNMExp versionedAccPrefixExp("[NX]M")
 #define versionedRefSeqNPExp versionedAccPrefixExp("[NX]P")
 #define versionedRefSeqNMRExp versionedAccPrefixExp("[NX][MR]")
 
 // Nucleotide position regexes
 // (c. = CDS, g. = genomic, m. = mitochondrial, n.= non-coding RNA, r. = RNA)
 #define posIntExp "([0-9]+)"
 #define hgvsGenoPosExp posIntExp "(_" posIntExp ")?"
 //                   ......                     1-based start position
 //                           .............      optional range separator and end position
 //                               ......         1-based end position
 // n. terms can have exonic anchor base and intron offset for both start and end:
 #define offsetExp "([-+])"
 // c. terms may also have a UTR indicator before the anchor base (- for UTR5, * for UTR3)