0926946a1fed476484b175c2c7ce40de2b4f4bf9
angie
  Fri Jun 30 10:44:46 2017 -0700
Prevent mapping warning (e.g. ref mismatch) from causing us to error out after parsing changes.

diff --git src/hg/lib/hgHgvs.c src/hg/lib/hgHgvs.c
index 47f37dd..fd30216 100644
--- src/hg/lib/hgHgvs.c
+++ src/hg/lib/hgHgvs.c
@@ -2124,30 +2124,35 @@
     {
     dyStringPrintf(dyError, "HGVS protein changes such as '%s' are ambiguous at the nucleotide "
                    "level, so not supported", term);
     return NULL;
     }
 struct dyString *dyWarn = dyStringNew(0);
 char *pslTable = NULL;
 struct bed *mapping = hgvsValidateAndMap(hgvs, db, term, dyWarn, &pslTable);
 if (!mapping)
     {
     dyStringPrintf(dyError, "Unable to map '%s' to reference %s: %s",
                    term, db, dyStringContents(dyWarn));
     }
 else
     {
+    if (dyStringIsNotEmpty(dyWarn))
+        {
+        dyStringAppend(dyError, dyStringContents(dyWarn));
+        dyStringClear(dyWarn);
+        }
     struct hgvsChange *changeList = hgvsParseNucleotideChange(hgvs->changes, hgvs->type,
                                                               dyWarn);
     if (dyStringIsNotEmpty(dyWarn))
         {
         dyStringPrintf(dyError, "Unable to parse HGVS description in '%s': %s",
                        term, dyStringContents(dyWarn));
         }
     else if (changeList->type == hgvsctRepeat)
         {
         dyStringPrintf(dyError,
                        "Can't convert '%s' to VCF: HGVS repeat notation is not supported.", term);
         }
     else
         {
         row = vcfFromHgvs(db, term, mapping, hgvs, changeList, doLeftShift, dyWarn);