bf2b4ab1b621fbcddc5b00c40616fdda09681942
angie
  Thu Sep 21 11:15:57 2017 -0700
Peter Causey-Freeman (VariantValidator.org) convinced me that Mutalyzer is overconfident in assigning p.= to variants in UTR, introns etc; safer to go with p.?.

diff --git src/hg/lib/hgHgvs.c src/hg/lib/hgHgvs.c
index f2f3b2d..43fc4e5 100644
--- src/hg/lib/hgHgvs.c
+++ src/hg/lib/hgHgvs.c
@@ -2571,33 +2571,31 @@
 if (addParens)
     dyStringAppendC(dy, '(');
 int refLen = vpPep->end - vpPep->start;
 // When predicting frameshift/extension, the length of ref may be different from refLen
 int refExtLen = vpPep->ref ? strlen(vpPep->ref) : refLen;
 int altLen = vpPep->alt ? strlen(vpPep->alt) : 0;
 char refStartAbbr[4];
 if (vpPep->ref)
     aaToAbbr(vpPep->ref[0], refStartAbbr, sizeof(refStartAbbr));
 else
     // If ref is null then we should be writing just '=' or '?' but prevent garbage just in case:
     safecpy(refStartAbbr, sizeof(refStartAbbr), "?");
 // protSeq may or may not end with X, so treat protSeq->size accordingly
 boolean hitsStopCodon = (vpPep->end > protSeq->size ||
                          ((protSeq->dna[protSeq->size-1] == 'X') && vpPep->end == protSeq->size));
-if (vpPep->likelyNoChange)
-    dyStringAppend(dy, "=");
-else if (vpPep->cantPredict || vpPep->spansUtrCds)
+if (vpPep->cantPredict || vpPep->spansUtrCds)
     dyStringAppend(dy, "?");
 else if (vpPep->frameshift)
     {
     dyStringPrintf(dy, "%s%d", refStartAbbr, vpPep->start+1);
     if (altLen == 1)
         dyStringAppend(dy, "Ter");
     else
         {
         char altStartAbbr[4];
         aaToAbbr(vpPep->alt[0], altStartAbbr, sizeof(altStartAbbr));
         // For stop-loss extension, make it "ext*"
         if (hitsStopCodon && altLen > refExtLen)
             dyStringPrintf(dy, "%sext*%d", altStartAbbr, altLen - refExtLen);
         else
             dyStringPrintf(dy, "%sfsTer%d", altStartAbbr, altLen);