diff --git a/bwa-typeHLA.js b/bwa-typeHLA.js
index 5561952..ad47387 100644
--- a/bwa-typeHLA.js
+++ b/bwa-typeHLA.js
@@ -195,14 +195,14 @@ for (var e = 0; e < exons.length; ++e) {
 		}
 	// drop mismapped contigs
 	var dropped = [];
-	for (var c = 0; c < ca.length; ++c) {
-		var min = 0x7fffffff, cc = ca[c];
-		for (var g = 0; g < ga.length; ++g) {
-			var gg = ga[g];
-			min = min < sc[gg][cc]? min : sc[gg][cc];
+	for (var k = 0; k < ca.length; ++k) {
+		var min = 0x7fffffff, c = ca[k];
+		for (var i = 0; i < ga.length; ++i) {
+			var g = ga[i];
+			min = min < sc[g][c]? min : sc[g][c];
 		}
-		dropped[cc] = min > drop_thres? true : false;
-		if (dropped[cc]) warn("Dropped contig " +clist[cc]+ " due to high divergence to all genes (minNM=" +min+ ")");
+		dropped[c] = min > drop_thres? true : false;
+		if (dropped[c]) warn("Dropped contig " +clist[c]+ " due to high divergence to all genes (minNM=" +min+ ")");
 	}
 	// fill the pair array
 	var min_nm = 0xffff;
@@ -211,7 +211,7 @@ for (var e = 0; e < exons.length; ++e) {
 		for (var j = i; j < ga.length; ++j) {
 			var gj = ga[j], g2 = sc[gj], m = 0;
 			for (var k = 0; k < ca.length; ++k) {
-				c = ca[k];
+				var c = ca[k];
 				if (!dropped[c])
 					m += g1[c] < g2[c]? g1[c] : g2[c];
 			}
diff --git a/bwa-typeHLA.sh b/bwa-typeHLA.sh
new file mode 100755
index 0000000..cc4bd12
--- /dev/null
+++ b/bwa-typeHLA.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+if [ $# -lt 2 ]; then
+	echo "Usage: $0 <prefix> <gene>"
+	exit 1
+fi
+
+root=`dirname $0`
+pre=$1.$2
+len=`$root/seqtk comp $pre.fq | awk '{++x;y+=$2}END{printf("%.0f\n", y/x)}'`
+
+$root/fermi2.pl unitig -t2 -l$len -p $pre.utg $pre.fq > $pre.utg.mak
+make -f $pre.utg.mak
+$root/bwa mem -B1 -O1 -E1 $root/HLA-ALT.fa $pre.utg.mag.gz | grep -v ^@ | sort -k3,3 -k4,4n | bgzip > $pre.utg.alt.gz
+$root/tabix -Bpsam $pre.utg.alt.gz $root/HLA-approx.anno | cut -f1 | sort | uniq | $root/seqtk subseq $pre.utg.mag.gz - | gzip -1 > $pre.utg.fq.gz
+rm $pre.utg.{flt,ec,raw,pre}.* $pre.utg.mag* $pre.utg.mak $pre.utg.alt.gz
+$root/bwa index -p $pre.utg $pre.utg.fq.gz
+$root/bwa mem -aD.1 -t2 $pre.utg $root/hla.fa | egrep "^(@|$2)" > $pre.utg.sam
+rm $pre.utg.{ann,amb,bwt,sa,pac}