--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/test/test_view.pl	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,71 @@
+#! /usr/bin/env perl
+#
+#    Copyright (C) 2013 Genome Research Ltd.
+#
+#    Author: James Bonfield <jkb@sanger.ac.uk>
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+use strict;
+use warnings;
+
+my $err_count = 0;
+my $suc_count = 0;
+
+sub test {
+    my ($cmd) = @_;
+    print "  $cmd\n";
+    if (system("$cmd || exit 1") != 0) {
+        print "FAIL $!\n";
+        $err_count++;
+    } else {
+        $suc_count++;
+    }
+}
+
+foreach my $sam (glob("*#*.sam")) {
+    my ($base, $ref) = ($sam =~ /((.*)#.*)\.sam/);
+    $ref .= ".fa";
+
+    my $bam  = "$base.tmp.bam";
+    my $cram = "$base.tmp.cram";
+
+    print "\n=== Testing $sam, ref $ref ===\n";
+
+    # SAM -> BAM -> SAM
+    test "./test_view -S -b $sam > $bam";
+    test "./test_view $bam > $bam.sam_";
+    test "./compare_sam.pl $sam $bam.sam_";
+
+    # SAM -> CRAM -> SAM
+    test "./test_view -t $ref -S -C $sam > $cram";
+    test "./test_view -D $cram > $cram.sam_";
+    test "./compare_sam.pl -nomd $sam $cram.sam_";
+
+    # BAM -> CRAM -> BAM -> SAM
+    $cram = "$bam.cram";
+    test "./test_view -t $ref -C $bam > $cram";
+    test "./test_view -b -D $cram > $cram.bam";
+    test "./test_view $cram.bam > $cram.bam.sam_";
+    test "./compare_sam.pl -nomd $sam $cram.bam.sam_";
+}
+
+print "\nSuccesses $suc_count\n";
+print "\nFailures  $err_count\n";
+
+exit ($err_count > 0);