7cd88510c60532d95aee9e98ba02d191990d873e
angie
  Sat Oct 15 20:34:05 2022 -0700
Fixing typo in corner case of writing alt alleles for VCF with imputed alleles, that caused segv when parsing the generated VCF. https://github.com/yatisht/usher/issues/282

diff --git src/hg/hgPhyloPlace/writeCustomTracks.c src/hg/hgPhyloPlace/writeCustomTracks.c
index 1ee0bde..eae53d6 100644
--- src/hg/hgPhyloPlace/writeCustomTracks.c
+++ src/hg/hgPhyloPlace/writeCustomTracks.c
@@ -128,31 +128,31 @@
                                     {
                                     if (alt->name[1] == '\0' && val[1] == '\0' &&
                                         isIupacAmbiguous(alt->name[0]))
                                         {
                                         char lowerV = tolower(val[0]);
                                         if (strchr(iupacAmbiguousToString(alt->name[0]), lowerV))
                                             {
                                             verbose(3,
                                                   "gtIx %d: val (%s) matches ambig alts[%d] (%s)\n",
                                                     gtIx, val, altIx, alt->name);
                                             // The alt is an ambiguous character that includes val.
                                             // Replace this alt with val.
                                             foundIt = TRUE;
                                             alt->name[0] = val[0];
                                             // Update the alts column
-                                            words[4] = slNameListToString(alts, '.');
+                                            words[4] = slNameListToString(alts, ',');
                                             int len = strlen(words[colIx]);
                                             safef(words[colIx], len+1, "%d", altIx+1);
                                             verbose(3, "gtIx %d: swapped in %s\n",
                                                     gtIx, words[colIx]);
                                             break;
                                             }
                                         }
                                     }
                                 if (!foundIt)
                                     {
                                     // Add the imputed value as a new alt.
                                     int altCount = slCount(alts);
                                     verbose(3, "gtIx %d: adding val as new alts[%d] = %s\n",
                                             gtIx, altCount, val);
                                     int len = strlen(words[colIx]);