3e70e7601a08e28667531d5abe3fe8b04ee95ded
chmalee
  Fri Jul 16 11:23:58 2021 -0700
Return multiple transcripts for pseudo hgvs search, refs #15554

diff --git src/hg/inc/hgHgvs.h src/hg/inc/hgHgvs.h
index 2314781..1c43023 100644
--- src/hg/inc/hgHgvs.h
+++ src/hg/inc/hgHgvs.h
@@ -167,31 +167,33 @@
 #define HGVS_OUT_P  0x04
 // Add parentheses around predicted protein (p.) changes e.g. p.(Arg159del):
 #define HGVS_OUT_P_ADD_PARENS 0x10
 // Add deleted sequence to delins changes (e.g. show 'delAGinsTT' instead of 'delinsTT'):
 #define HGVS_OUT_BREAK_DELINS 0x20
 
 
 void hgvsVariantFree(struct hgvsVariant **pHgvs);
 // Free *pHgvs and its contents, and set *pHgvs to NULL.
 
 struct hgvsVariant *hgvsParseTerm(char *term);
 /* If term is a parseable form of HGVS, return the parsed representation, otherwise NULL.
  * This does not check validity of accessions or alleles. */
 
 struct hgvsVariant *hgvsParsePseudoHgvs(char *db, char *term);
-/* Attempt to parse things that are not strict HGVS, but that people might intend as HGVS. */
+/* Attempt to parse things that are not strict HGVS, but that people might intend as HGVS:
+ * Return a list of struct hgvsVariant that may be what was intended  */
+// Note: this doesn't support non-coding gene symbol terms (which should have nt alleles)
 
 boolean hgvsValidate(char *db, struct hgvsVariant *hgvs, char **retFoundAcc, int *retFoundVersion,
                      char **retDiffRefAllele);
 /* Return TRUE if hgvs coords are within the bounds of the sequence for hgvs->seqAcc.
  * Note: Transcript terms may contain coords outside the bounds (upstream, intron, downstream) so
  * those can't be checked without mapping the term to the genome; this returns TRUE if seq is found.
  * If retFoundAcc is not NULL, set it to our local accession (which may be missing the .version
  * of hgvs->seqAcc) or NULL if we can't find any match.
  * If retFoundVersion is not NULL and hgvs->seqAcc has a version number (e.g. NM_005957.4),
  * set retFoundVersion to our version from latest GenBank, otherwise 0 (no version for LRG).
  * If coords are OK and retDiffRefAllele is not NULL: if our sequence at the coords
  * matches hgvs->refAllele then set it to NULL; if mismatch then set it to our sequence. */
 
 struct bed *hgvsMapToGenome(char *db, struct hgvsVariant *hgvs, char **retPslTable);
 /* Return a bed6 with the variant's span on the genome and strand, or NULL if unable to map.