[med-svn] [paleomix] 01/08: Somehow also test bwa - not finished

[Andreas Tille]

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tille pushed a commit to branch master
in repository paleomix.

commit 3ec2633dbb17cf0cba2e4707695224ef952c2c7b
Author: Andreas Tille <tille at debian.org>
Date:   Wed Feb 22 17:18:19 2017 +0100

    Somehow also test bwa - not finished
---
 debian/tests/bwa/run.sh | 89 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 89 insertions(+)

diff --git a/debian/tests/bwa/run.sh b/debian/tests/bwa/run.sh
new file mode 100644
index 0000000..924228f
--- /dev/null
+++ b/debian/tests/bwa/run.sh
@@ -0,0 +1,89 @@
+#!/bin/bash
+# this is a rough edit of upstreams tests/bwa/run.sh to make
+# it somehow working.  It definitely needs more care (FIXME!)
+# to make it a real test
+
+set -o nounset # Fail on unset variables
+set -o errexit # Fail on uncaught non-zero returncodes
+set -o pipefail # Fail is a command in a chain of pipes fails
+
+echo cd $(dirname $0)
+
+# Errors to ignore during valiation
+IGNORE="IGNORE=RECORD_MISSING_READ_GROUP IGNORE=MISSING_READ_GROUP"
+
+ls -d testcases/* |
+while read testcase;
+do
+	echo "Running testcase ${testcase}: $(head -n1 ${testcase}/README)"
+	mkdir -p debian
+	ln -sf /usr/bin/bwa debian
+	readlink debian/bwa |
+	while read BWA;
+	do
+		echo -n "  $BWA "
+
+		rm -rf temp
+        folder="runs/$testcase/$(dirname $BWA | xargs basename)"
+        rm -rf $folder
+        mkdir -p $folder
+        ln -s $folder temp
+
+		msg=""
+		returncode=-1
+
+		cp ${testcase}/* temp/
+		if [ -e "temp/run.sh" ];
+		then
+			bash "temp/run.sh" "/usr/bin/bwa" && returncode=$? || returncode=$?
+
+			if [ -e "temp/run.log" ];
+			then
+				msg="$(head -n1 temp/run.log)"
+			fi
+		elif [ -e "temp/reads1.fasta" ];
+		then
+			PREFIX=temp/prefix.fasta
+			READS1=temp/reads1.fasta
+			READS2=temp/reads2.fasta
+			RESULTS=temp/results
+
+            command="index"
+			if $BWA index ${PREFIX} 2> ${PREFIX}.log;
+			then
+                command="aln #1"
+				if $BWA aln ${PREFIX} ${READS1} > ${READS1}.fai 2> ${READS1}.log;
+				then
+                    command="aln #2"
+					if $BWA aln ${PREFIX} ${READS2} > ${READS2}.fai 2> ${READS2}.log;
+					then
+                        command="sampe"
+						if $BWA sampe ${PREFIX} ${READS1}.fai ${READS2}.fai ${READS1} ${READS2} 2> ${RESULTS}.log | \
+							paleomix cleanup --paired --fasta ${PREFIX} --temp-prefix temp/cleanup 2> ${RESULTS}.cleanup.log >  ${RESULTS}.bam;
+						then
+							java -jar "ValidateSamFile.jar" ${IGNORE} I=${RESULTS}.bam &> ${RESULTS}.bam.validated \
+								&& returncode=$? || returncode=$?
+
+							if [ -e "${RESULTS}.bam.validated" ];
+							then
+								msg="$((grep ERROR ${RESULTS}.bam.validated || true) | head -n1)"
+							fi
+						fi
+					fi
+				fi
+			fi
+		fi
+
+		if test $returncode -eq 0;
+		then
+			echo -e "\033[32m[OK]\033[0m"
+		elif test $returncode -eq -1;
+		then
+			echo -e "\033[31m[TEST ERROR]: $command\033[0m"
+		else
+			echo -e "\033[33m[FAILED]\033[0m: $msg"
+		fi
+	done
+done
+
+rm -rf temp

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