7898951baf0f75614898e4d6ff735c444f46cbb5
angie
  Wed Oct 5 11:25:44 2011 -0700
Fixed an incorrect regex substr index for VCF FILTER or ALT header defs.
diff --git src/lib/vcf.c src/lib/vcf.c
index 0b8bc81..26ad918 100644
--- src/lib/vcf.c
+++ src/lib/vcf.c
@@ -302,34 +302,34 @@
 	else
 	    def->fieldCount = atoi(line + substrs[3].rm_so);
 	def->type = vcfInfoTypeFromSubstr(vcff, line, substrs[4]);
 	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[3] is Description.
+	// substrs[2] is ID/key, substrs[4] is Description.
 	struct vcfInfoDef *def = vcfFileAlloc(vcff, sizeof(struct vcfInfoDef));
 	def->key = vcfFileCloneSubstr(vcff, line, substrs[2]);
-	def->description = vcfFileCloneSubstr(vcff, line, substrs[3]);
+	def->description = vcfFileCloneSubstr(vcff, line, substrs[4]);
 	slAddHead((isFilter ? &(vcff->filterDefs) : &(vcff->altDefs)), def);
 	}
     else
 	vcfFileErr(vcff, "##%s line does not match expected pattern /%s/: \"%s\"",
 		   (isFilter ? "FILTER" : "ALT"), filterOrAltRegex, line);
     }
 }
 
 static void expectColumnName2(struct vcfFile *vcff, char *exp1, char *exp2, char *words[], int ix)
 /* Every file must include a header naming the columns, though most column names are
  * fixed; make sure the names of fixed columns are as expected. */
 {
 if (! sameString(exp1, words[ix]))
     {
     if (exp2 == NULL)