9a49290fedc8b4f9c7a631dedcfe8ac3aa2b4cee
chinhli
  Thu Oct 20 14:10:43 2011 -0700
merge conflict resolved
diff --git src/lib/vcf.c src/lib/vcf.c
index b5202e1..0fe7ef2 100644
--- src/lib/vcf.c
+++ src/lib/vcf.c
@@ -294,30 +294,33 @@
     nonAsciiWorkaround(line);
     if (regexMatchSubstr(line, infoOrFormatRegex, substrs, ArraySize(substrs)))
 	// substrs[2] is ID/key, substrs[3] is Number, [4] is Type and [5] is Description.
 	{
 	struct vcfInfoDef *def = vcfFileAlloc(vcff, sizeof(struct vcfInfoDef));
 	def->key = vcfFileCloneSubstr(vcff, line, substrs[2]);
 	char *number = vcfFileCloneSubstr(vcff, line, substrs[3]);
 	if (sameString(number, ".") || sameString(number, "A") || sameString(number, "G"))
 	    // A is #alts which varies line-to-line; "G" is #genotypes which we haven't
 	    // yet seen.  Why is there a G here -- shouldn't such attributes go in the
 	    // genotype columns?
 	    def->fieldCount = -1;
 	else
 	    def->fieldCount = atoi(number);
 	def->type = vcfInfoTypeFromSubstr(vcff, line, substrs[4]);
+	// greedy regex pulls in end quote, trim if found:
+	if (line[substrs[5].rm_eo-1] == '"')
+	    line[substrs[5].rm_eo-1] = '\0';
 	def->description = vcfFileCloneSubstr(vcff, line, substrs[5]);
 	slAddHead((isInfo ? &(vcff->infoDefs) : &(vcff->gtFormatDefs)), def);
 	}
     else
 	vcfFileErr(vcff, "##%s line does not match expected pattern /%s/: \"%s\"",
 		   (isInfo ? "INFO" : "FORMAT"), infoOrFormatRegex, line);
     }
 else if (startsWith("##FILTER=", line) || startsWith("##ALT=", line))
     {
     boolean isFilter = startsWith("##FILTER", line);
     if (regexMatchSubstr(line, filterOrAltRegex, substrs, ArraySize(substrs)))
 	{
 	// substrs[2] is ID/key, substrs[4] is Description.
 	struct vcfInfoDef *def = vcfFileAlloc(vcff, sizeof(struct vcfInfoDef));
 	def->key = vcfFileCloneSubstr(vcff, line, substrs[2]);