fix workflow and scripts

test/test_eventalign_pafsam.sh

@@ -25,27 +25,50 @@ download_test_set() {
 	rm -f $tar_path
 }
 
+
+
+handle_tests() {
+	numfailed=$(wc -l < ${testdir}/diff.txt)
+	numcases=$(wc -l < ${ORIG})
+	numres=$(wc -l < ${RES})
+	echo "$numfailed of $numcases test cases deviated."
+	missing=$(echo "$numcases-$numres" | bc)
+	echo "$missing entries in the truthset are missing in the testset"
+	failp=$(echo "$numfailed*100/$numcases" | bc)
+	[ "$failp" -gt ${THRESH} ] && die "${1}: Validation failed"
+	echo "Validation passed"
+}
+
+execute_test() {
+
+	ORIG=$2
+	RES=$1
+	THRESH=5
+	diff -y --suppress-common-lines ${ORIG} ${RES} > ${testdir}/diff.txt || handle_tests $testdir
+
+}
+
 testdir=test/hg2_lsk114_reads_1000
 download_test_set "https://f5c.page.link/hg2_lsk114_reads_1000"
 
 ./f5c eventalign -b ${testdir}/PGXX22394_reads_1000_6.4.2_sup.bam \
 		-r ${testdir}/PGXX22394_reads_1000_6.4.2_sup.fastq -g test/chr22_meth_example/humangenome.fa \
 		--slow5 ${testdir}/PGXX22394_reads_1000.blow5 -c > ${testdir}/result.txt || die "eventalign failed"
-diff -q ${testdir}/result.txt ${testdir}/eventalign.paf || die "eventalign failed"
+execute_test ${testdir}/result.txt ${testdir}/eventalign.paf
 
 ./f5c eventalign -b ${testdir}/PGXX22394_reads_1000_6.4.2_sup.bam \
 		-r ${testdir}/PGXX22394_reads_1000_6.4.2_sup.fastq -g test/chr22_meth_example/humangenome.fa \
 		--slow5 ${testdir}/PGXX22394_reads_1000.blow5 -a > ${testdir}/result.txt || die "eventalign failed"
-diff -q ${testdir}/result.txt ${testdir}/eventalign.sam || die "eventalign failed"
+execute_test ${testdir}/result.txt ${testdir}/eventalign.sam
 
 
 testdir=test/rna
-download_test_set "https://f5c.page.link/rna"
+download_test_set "https://f5c.page.link/f5c_rna_test"
 
 ./f5c eventalign -b ${testdir}/reads.sorted.bam -g ${testdir}/gencode.v35.transcripts.fa -r ${testdir}//reads.fastq  \
  --slow5 ${testdir}/reads.blow5 --rna -c > ${testdir}/result.txt || die "eventalign failed"
-diff -q ${testdir}/result.txt ${testdir}/eventalign.paf || die "eventalign failed"
+execute_test ${testdir}/result.txt ${testdir}/eventalign.paf
 
 ./f5c eventalign -b ${testdir}/reads.sorted.bam -g ${testdir}/gencode.v35.transcripts.fa -r ${testdir}//reads.fastq  \
  --slow5 ${testdir}/reads.blow5 --rna -a > ${testdir}/result.txt || die "eventalign failed"
-diff -q ${testdir}/result.txt ${testdir}/eventalign.sam || die "eventalign failed"
+execute_test ${testdir}/result.txt ${testdir}/eventalign.sam