Add test files for mmFlagModifier

c/c_tests/test_05_mmFlagModifier.sh

@@ -0,0 +1,107 @@
+#!/bin/bash
+
+##########LICENCE##########
+# PCAP - NGS reference implementations and helper code for the ICGC/TCGA Pan-Cancer Analysis Project
+# Copyright (C) 2014-2019 Genome Research Limited
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not see:
+#   http://www.gnu.org/licenses/gpl-2.0.html
+##########LICENCE##########
+
+compare_sam () {
+  sam1 = $1;
+  sam2 = $2;
+  #Cut out the header and sort from first sam
+  grep -e '^@' $1 | perl -aple '@F=sort @F;$_=join qq{\t},@F;' > $1.tmphead
+  #Cut out the header and sort from second sam
+  grep -e '^@' $2 | perl -aple '@F=sort @F;$_=join qq{\t},@F;' > $2.tmphead
+  diff $1.tmphead  $2.tmphead
+  if [ "$?" != "0" ];
+  then
+    echo "ERROR in "$0": Comparing headers of sam files $1 and $2."
+    return 1
+  fi
+  rm $1.tmphead $2.tmphead
+  grep -ve '^@' $1 > $1.tmpreads
+  grep -ve '^@' $2 > $2.tmpreads
+  diff $1.tmpreads $2.tmpreads
+  if [ "$?" != "0" ];
+  then
+    echo "ERROR in "$0": Comparing reads of sam files $1 and $2."
+    return 1
+  fi
+  rm $1.tmpreads $2.tmpreads
+  return 0
+}
+
+#Ensure valid format produced
+../bin/mmFlagModifier -i ../t/data/mismatch_test.bam -m | bamvalidate
+if [ "$?" != "0" ];
+then
+  echo "ERROR running ../bin/mmFlagModifier -i ../t/data/mismatch_test.bam -m . Invalid output"
+  exit 1;
+fi
+
+../bin/mmFlagModifier -i ../t/data/mismatch_test.bam -p | bamvalidate
+if [ "$?" != "0" ];
+then
+  echo "ERROR running ../bin/mmFlagModifier -i ../t/data/mismatch_test.bam -p. Invalid output"
+  exit 1;
+fi
+
+../bin/mmFlagModifier -i ../t/data/mismatch_test.cram -C -m | bamvalidate inputformat=cram
+if [ "$?" != "0" ];
+then
+  echo "ERROR running ../bin/mmFlagModifier -i ../t/data/mismatch_test.bam -C. Invalid output cram compression"
+  exit 1;
+fi
+
+../bin/mmFlagModifier -i ../t/data/mismatch_test.cram -C -p | bamvalidate inputformat=cram
+if [ "$?" != "0" ];
+then
+  echo "ERROR running ../bin/mmFlagModifier -i ../t/data/mismatch_test.bam -C. Invalid output cram compression"
+  exit 1;
+fi
+
+../bin/mmFlagModifier -i ../t/data/mismatch_test.bam -m | bamcollate2 inputformat=bam outputformat=sam collate=0 resetaux=0 > ../t/data/mmFlagModifier_test_out.sam;
+if [ "$?" != "0" ];
+then
+  echo "ERROR running ../bin/mmFlagModifier -i ../t/data/mismatch_test.bam -m | bamcollate2 inputformat=bam outputformat=sam collate=0 resetaux=0 > ../t/data/mmFlagModifier_test_out.sam"
+  exit 1;
+fi
+
+if [ compare_sam '../t/data/mmFlagModifier_test_out.sam' '../t/data/mmFlagModifier_m_expected_out.sam' != "0" ];
+then
+  echo "ERROR in "$0": Comparing mmFlagModifier to expected result failed."
+	echo "------"
+	rm ../t/data/mmFlagModifier_test_out.sam
+  exit 1
+fi
+
+../bin/mmFlagModifier -i ../t/data/mmFlagModifier_p_input.bam -p | bamcollate2 inputformat=bam outputformat=sam collate=0 resetaux=0 > ../t/data/mmFlagModifier_test_out.sam;
+if [ "$?" != "0" ];
+then
+  echo "ERROR running ../bin/mmFlagModifier -i ../t/data/mismatch_test.bam -p | bamcollate2 inputformat=bam outputformat=sam collate=0 resetaux=0 > ../t/data/mmFlagModifier_test_out.sam"
+  exit 1;
+fi
+
+if [ compare_sam '../t/data/mmFlagModifier_test_out.sam' '../t/data/mismatch_expected_out.sam' != "0" ];
+then
+  echo "ERROR in "$0": Comparing mmFlagModifier to expected result failed."
+	echo "------"
+	rm ../t/data/mmFlagModifier_test_out.sam
+  exit 1
+fi
+
+rm ../t/data/mmFlagModifier_test_out.sam