d9aba93eae9c9c1ba3f09055db42843cec8d63ba
angie
  Wed Mar 6 17:09:07 2019 -0800
Restoring a line incorrectly deleted in 49a9e46 -- thanks Braney for spotting!  refs #23051

diff --git src/lib/annoStreamVcf.c src/lib/annoStreamVcf.c
index 0c77235..4b8de8a 100644
--- src/lib/annoStreamVcf.c
+++ src/lib/annoStreamVcf.c
@@ -150,30 +150,31 @@
 	lineFileSetTabixRegion(self->vcff->lf, regionChrom, regionStart, regionEnd);
         rowChrom = regionChrom;
 	}
     // Skip to next row if this is on a previous chromosome, or is on regionChrom but
     // ends before regionStart or ends at regionStart and is not an insertion.
     struct vcfRecord *rec = self->record;
     while (words != NULL &&
 	   (strcmp(rowChrom, regionChrom) < 0 ||
 	    (sameString(rowChrom, regionChrom) &&
              (rec->chromEnd < regionStart ||
               (rec->chromStart != rec->chromEnd && rec->chromEnd == regionStart)))))
         {
 	words = nextRowRaw(self);
         if (words == NULL)
             break;
+        rowChrom = getProperChromName(self, words[0]);
         rec = self->record;
         }
     }
 // Tabix doesn't give us any rows past end of region, but if not using tabix,
 // detect when we're past end of region.  It's possible for a non-indel to precede
 // an insertion that has the same VCF start coord but is actually to its left,
 // so we can't just quit as soon as we see anything with chromStart == regionEnd.
 if (words != NULL && !self->isTabix && sSelf->chrom != NULL
     && self->record->chromStart > sSelf->regionEnd)
     {
     words = NULL;
     self->record = NULL;
     }
 if (words != NULL)
     self->recordCount++;