f01188d126fc6c9318f579ad1bcdf0ad392b9187
angie
  Thu Apr 17 11:33:18 2014 -0700
There was one more place where I needed to prepend "chr" to a VCFsequence name when comparing to region chrom.
fixes #13093

diff --git src/lib/annoStreamVcf.c src/lib/annoStreamVcf.c
index 5ca977c..141c33f 100644
--- src/lib/annoStreamVcf.c
+++ src/lib/annoStreamVcf.c
@@ -113,40 +113,41 @@
 if (minChrom != NULL)
     {
     if (regionChrom == NULL)
 	{
 	regionChrom = minChrom;
 	regionStart = minEnd;
 	}
     else
 	{
 	regionStart = max(regionStart, minEnd);
 	}
     }
 char **words = nextRowRaw(self);
 if (regionChrom != NULL && words != NULL)
     {
-    if (self->isTabix && strcmp(getProperChromName(self, words[0]), regionChrom) < 0)
+    char *rowChrom = getProperChromName(self, words[0]);
+    if (self->isTabix && strcmp(rowChrom, regionChrom) < 0)
 	{
 	uint regionEnd = sSelf->regionEnd;
 	if (minChrom != NULL && sSelf->chrom == NULL)
 	    regionEnd = annoAssemblySeqSize(sSelf->assembly, minChrom);
 	lineFileSetTabixRegion(self->vcff->lf, regionChrom, regionStart, regionEnd);
 	}
     while (words != NULL &&
-	   (strcmp(getProperChromName(self, words[0]), regionChrom) < 0 ||
-	    (sameString(words[0], regionChrom) && self->record->chromEnd < regionStart)))
+	   (strcmp(rowChrom, regionChrom) < 0 ||
+	    (sameString(rowChrom, regionChrom) && self->record->chromEnd < regionStart)))
 	words = nextRowRaw(self);
     }
 // Tabix doesn't give us any rows past end of region, but if not using tabix,
 // detect when we're past end of region:
 if (words != NULL && !self->isTabix && sSelf->chrom != NULL
     && self->record->chromStart > sSelf->regionEnd)
     {
     words = NULL;
     self->record = NULL;
     }
 if (words != NULL)
     self->recordCount++;
 if (words == NULL || (self->maxRecords > 0 && self->recordCount >= self->maxRecords))
     self->eof = TRUE;
 return words;