--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bsf-call_wrapper.pl	Sun Apr 19 20:51:13 2015 +0900
@@ -0,0 +1,51 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use FindBin;
+
+print STDOUT "The tool script is called with:\n", join(" ", ($0, @ARGV)), "\n\n";
+
+my ($idx, $in) = ("", "");
+my $default_option = "-o bsf-call.out -W bsfwork";
+
+my $tooldir = shift(@ARGV);
+$tooldir = $FindBin::Bin;
+$ENV{PATH} = "$tooldir/bin:" . $ENV{PATH};
+my $reference_source = shift(@ARGV);
+my $read_end = shift(@ARGV);
+my $gslot = shift(@ARGV);
+#$idx = "$tooldir/data/chrX.sub.fa";
+
+if ($reference_source eq "indexed") {
+    $idx = shift(@ARGV);
+}
+elsif ($reference_source eq "history") {
+    my $own = shift(@ARGV);
+    $idx = "reference.fa";
+    &invoke_command("ln -s $own reference.fa");
+}
+else {
+    die "never reach here\n";
+}
+
+if ($read_end eq "single-end") {
+    $in = shift(@ARGV);
+    &invoke_command("$tooldir/bin/bsf-call $default_option -p $gslot $idx $in");
+}
+elsif ($read_end eq "paired-end") {
+    my $in1 = shift(@ARGV);
+    my $in2 = shift(@ARGV);
+    $in = $in1 . "," . $in2;
+    &invoke_command("$tooldir/bin/bsf-call $default_option -p $gslot $idx $in");
+}
+else {
+    die "never reach here\n";
+}
+
+sub invoke_command {
+    my ($command) = @_;
+    print "invoking: $command\n";
+    system($command);
+}