move test scripts to test

Makefile

@@ -202,4 +202,4 @@ test: $(BINARY)
 	./scripts/test.sh
 
 test_eventalign: $(BINARY)
-	./scripts/test_eventalign.sh
+	./test/test_eventalign.sh

scripts/test_eventalign.sh → test/test_eventalign.sh

@@ -98,7 +98,7 @@ execute_test() {
 	tail -n +2 ${testdir}/f5c_event_align.summary.txt | awk '{print $1"\t"$2"\t"$3"\tna\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12"\t"$13"\t"$14}' > ${testdir}/f5c.summary.txt
 	#this test still passes if f5c.summary.txt is empty, but will be caught when comparing full summaries
 	join ${testdir}/nanopolish.summary.txt ${testdir}/f5c.summary.txt > ${testdir}/joined_results.txt || echo "Join ran into an issue. Probably just a warning."
-	awk -f  scripts/test_eventalign_summary.awk ${testdir}/joined_results.txt > ${testdir}/joined_diff.txt || handle_tests "${file}"
+	awk -f  test/test_eventalign_summary.awk ${testdir}/joined_results.txt > ${testdir}/joined_diff.txt || handle_tests "${file}"
 
 	if [ $testdir = test/chr22_meth_example ]; then
 		echo "event by event test not implemented not yet implemented!"
@@ -115,7 +115,7 @@ execute_test() {
 		tail -n +2 ${testdir}/result.txt  > ${testdir}/f5c.txt
 		#todo : this must be fixed for join with two columns ideally
 		paste ${testdir}/nanopolish.txt ${testdir}/f5c.txt > ${testdir}/joined_results.txt
-		awk -f  scripts/test_eventalign.awk ${testdir}/joined_results.txt > ${testdir}/joined_diff.txt || handle_tests2 "${file}"
+		awk -f  test/test_eventalign.awk ${testdir}/joined_results.txt > ${testdir}/joined_diff.txt || handle_tests2 "${file}"
 	fi
 
 
@@ -142,6 +142,7 @@ help_msg() {
 	echo
 	echo "-c                   Uses chr22_meth_example test set."
 	echo "-e                   Uses rna test set."
+	echo "-f                   Uses hg2 datase."
 	echo "-b [bam file]        Same as f5c -b."
 	echo "-K [n]               Same as f5c -K."
 	echo "-B [n]               Same as f5c -B."

scripts/test_eventalign_parameters.sh → test/test_eventalign_parameters.sh

@@ -69,13 +69,13 @@ execute_test() {
 	tail -n +2 ${testdir}/eventalign.summary.exp | awk '{print $1"\t"$2"\t"$3"\tdna\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12"\t"$13}' > ${testdir}/nanopolish.summary.txt
 	tail -n +2 ${testdir}/f5c_event_align.summary.txt | awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12"\t"$13"\t"$14}' > ${testdir}/f5c.summary.txt
 	join ${testdir}/nanopolish.summary.txt ${testdir}/f5c.summary.txt > ${testdir}/joined_results.txt || echo "Join ran into an issue. Probably just a warning."
-	awk -f  scripts/test_eventalign_summary.awk ${testdir}/joined_results.txt > ${testdir}/joined_diff.txt || handle_tests "${testdir}/joined_diff.txt"
+	awk -f  test/test_eventalign_summary.awk ${testdir}/joined_results.txt > ${testdir}/joined_diff.txt || handle_tests "${testdir}/joined_diff.txt"
 
 	echo "----------------comparing full results--------------"
 	tail -n +2 ${testdir}_big_testresults/$1  > ${testdir}/nanopolish.txt
 	tail -n +2 ${testdir}/result.txt  > ${testdir}/f5c.txt
 	paste ${testdir}/nanopolish.txt ${testdir}/f5c.txt > ${testdir}/joined_results.txt
-	awk -f  scripts/$2 ${testdir}/joined_results.txt > ${testdir}/joined_diff.txt || handle_tests2 "${testdir}/joined_diff.txt" $3
+	awk -f  test/$2 ${testdir}/joined_results.txt > ${testdir}/joined_diff.txt || handle_tests2 "${testdir}/joined_diff.txt" $3
 
 
 }

scripts/test_extensive.sh → test/test_extensive.sh

@@ -63,16 +63,16 @@ test_suit1 () {
 	scripts/test.sh 2> ecoli_methcalling.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "event alignment"
-	scripts/test_eventalign.sh 2> ecoli_eventalign.log || die "failed"
+	test/test_eventalign.sh 2> ecoli_eventalign.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "methylation frequency"
-	scripts/test_methfreq.sh 2> ecoli_methfreq.log || die "failed"
+	test/test_methfreq.sh 2> ecoli_methfreq.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "multi-fast5"
-	scripts/test_multifast5.sh 2> ecoli_multifast5.log  || die "failed"
+	test/test_multifast5.sh 2> ecoli_multifast5.log  || die "failed"
 	echo "____________________________________________________________________"
 	echo "index"
-	scripts/test_index.sh 2> ecoli_index.log || die "failed"
+	test/test_index.sh 2> ecoli_index.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "valgrind methcall"
 	scripts/test.sh valgrind 2> valgrind_methcall.log || die "failed"
@@ -81,19 +81,19 @@ test_suit1 () {
 	scripts/test.sh custom --kmer-model test/r9-models/r9.4_450bps.nucleotide.6mer.template.model --meth-model test/r9-models/r9.4_450bps.cpg.6mer.template.model 2> custom_6mer_methcall.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "slow5"
-	scripts/test_slow5.sh 2> ecoli_slow5.log || die "failed"
+	test/test_slow5.sh 2> ecoli_slow5.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "valgrind slow5"
-	scripts/test_slow5.sh valgrind 2> valgrind_slow5.log || die "failed"
+	test/test_slow5.sh valgrind 2> valgrind_slow5.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "vbz"
-	scripts/test_vbz.sh 2> ecoli_vbz.log || die "failed"
+	test/test_vbz.sh 2> ecoli_vbz.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "resquiggle"
-	scripts/test_rsq.sh 2> ecoli_resquiggle.log || die "failed"
+	test/test_rsq.sh 2> ecoli_resquiggle.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "resquiggle valgrind"
-	scripts/test_rsq.sh valgrind 2> ecoli_resquiggle_valgrind.log || die "failed"
+	test/test_rsq.sh valgrind 2> ecoli_resquiggle_valgrind.log || die "failed"
 	echo "____________________________________________________________________"
 
 	echo ""
@@ -105,41 +105,41 @@ test_suit1 () {
 	scripts/test.sh -c 2> na12878_methcalling.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "event alignment"
-	scripts/test_eventalign.sh -c 2> na12878_eventalign.log || die "failed"
+	test/test_eventalign.sh -c 2> na12878_eventalign.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "methylation frequency"
-	scripts/test_methfreq.sh -c 2> na12878_methfreq.log || die "failed"
+	test/test_methfreq.sh -c 2> na12878_methfreq.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "multi-fast5"
-	scripts/test_multifast5.sh -c 2> na12878_multifast5.log || die "failed"
+	test/test_multifast5.sh -c 2> na12878_multifast5.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "index"
-	scripts/test_index.sh -c 2> na12878_index.log || die "failed"
+	test/test_index.sh -c 2> na12878_index.log || die "failed"
 	echo ""
 	echo "____________________________________________________________________"
 	echo "slow5"
-	scripts/test_slow5.sh -c 2> na12878_slow5.log || die "failed"
+	test/test_slow5.sh -c 2> na12878_slow5.log || die "failed"
 
 	echo "************************Doing RNA tests*****************************"
 	echo "event alignment"
-	scripts/test_eventalign.sh -e 2> rna_eventalign.log || die "failed"
+	test/test_eventalign.sh -e 2> rna_eventalign.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "valgrind eventalign"
-	scripts/test_eventalign.sh -e valgrind 2> valgrind_rna_eventalign.log || die "failed"
+	test/test_eventalign.sh -e valgrind 2> valgrind_rna_eventalign.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "resquiggle"
-	scripts/test_rsq.sh -e 2> rna_resquiggle.log || die "failed"
+	test/test_rsq.sh -e 2> rna_resquiggle.log || die "failed"
 
 
 	echo "************************Doing R10 HG2 tests*****************************"
 	echo "Methylation calling"
 	scripts/test.sh -f 2> r10_hg2_methcalling.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "event alignment"
-	scripts/test_eventalign.sh -f 2> r10_hg2_eventalign.log || die "failed"
+	test/test_eventalign.sh -f 2> r10_hg2_eventalign.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "resquiggle"
-	scripts/test_rsq.sh -f 2> r10_hg2_resquiggle.log || die "failed"
+	test/test_rsq.sh -f 2> r10_hg2_resquiggle.log || die "failed"
 
 	echo ""
 	echo "*********************************************************************"
@@ -156,19 +156,19 @@ test_suit1_cuda () {
 	scripts/test.sh 2> ecoli_methcalling_cuda.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "event alignment"
-	scripts/test_eventalign.sh 2> ecoli_eventalign_cuda.log || die "failed"
+	test/test_eventalign.sh 2> ecoli_eventalign_cuda.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "methylation frequency"
-	scripts/test_methfreq.sh 2> ecoli_methfreq_cuda.log || die "failed"
+	test/test_methfreq.sh 2> ecoli_methfreq_cuda.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "multi-fast5"
-	scripts/test_multifast5.sh 2> ecoli_multifast5_cuda.log  || die "failed"
+	test/test_multifast5.sh 2> ecoli_multifast5_cuda.log  || die "failed"
 	echo "____________________________________________________________________"
 	echo "slow5"
-	scripts/test_slow5.sh 2> ecoli_slow5_cuda.log || die "failed"
+	test/test_slow5.sh 2> ecoli_slow5_cuda.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "resquiggle"
-	scripts/test_rsq.sh 2> ecoli_resquiggle_cuda.log || die "failed"
+	test/test_rsq.sh 2> ecoli_resquiggle_cuda.log || die "failed"
 	echo "____________________________________________________________________"
 
 	echo ""
@@ -180,38 +180,38 @@ test_suit1_cuda () {
 	scripts/test.sh -c 2> na12878_methcalling_cuda.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "event alignment"
-	scripts/test_eventalign.sh -c 2> na12878_eventalign_cuda.log || die "failed"
+	test/test_eventalign.sh -c 2> na12878_eventalign_cuda.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "methylation frequency"
-	scripts/test_methfreq.sh -c 2> na12878_methfreq_cuda.log || die "failed"
+	test/test_methfreq.sh -c 2> na12878_methfreq_cuda.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "multi-fast5"
-	scripts/test_multifast5.sh -c 2> na12878_multifast5_cuda.log || die "failed"
+	test/test_multifast5.sh -c 2> na12878_multifast5_cuda.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "slow5"
-	scripts/test_slow5.sh -c 2> na12878_slow5_cuda.log || die "failed"
+	test/test_slow5.sh -c 2> na12878_slow5_cuda.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "resquiggle"
-	scripts/test_rsq.sh -c 2> na12878_resquiggle_cuda.log || die "failed"
+	test/test_rsq.sh -c 2> na12878_resquiggle_cuda.log || die "failed"
 
 
 	echo "************************Doing RNA tests*****************************"
 	echo "event alignment"
-	scripts/test_eventalign.sh -e 2> rna_eventalign_cuda.log || echo "failure ignored until paste is implemented with join in full event align output"
+	test/test_eventalign.sh -e 2> rna_eventalign_cuda.log || echo "failure ignored until paste is implemented with join in full event align output"
 	echo "____________________________________________________________________"
 	echo "resquiggle"
-	scripts/test_rsq.sh -e 2> rna_resquiggle_cuda.log || die "failed"
+	test/test_rsq.sh -e 2> rna_resquiggle_cuda.log || die "failed"
 
 
 	echo "************************Doing R10 HG2 tests*****************************"
 	echo "Methylation calling"
 	scripts/test.sh -f 2> r10_hg2_methcalling_cuda.log || die "failed"
 	echo "____________________________________________________________________"
 	echo "event alignment"
-	scripts/test_eventalign.sh -f 2> r10_hg2_eventalign_cuda.log || echo "failure ignored for now until smaller diffs are accounted"
+	test/test_eventalign.sh -f 2> r10_hg2_eventalign_cuda.log || echo "failure ignored for now until smaller diffs are accounted"
 	echo "____________________________________________________________________"
 	echo "resquiggle"
-	scripts/test_rsq.sh -f 2> r10_hg2_resquiggle.log || die "failed"
+	test/test_rsq.sh -f 2> r10_hg2_resquiggle.log || die "failed"
 
 	echo ""
 	echo "*********************************************************************"
@@ -303,12 +303,12 @@ test_suit_eventalign_extra () {
 	echo "************************event align extra tests**********************"
 
 	echo "Event align parameter tests"
-	scripts/test_eventalign_parameters.sh 2> event_align_parameters.txt || die "failed"
+	test/test_eventalign_parameters.sh 2> event_align_parameters.txt || die "failed"
 	echo ""
 	echo "____________________________________________________________________"
 
 	echo "valgrind test"
-	scripts/test_eventalign.sh valgrind 2> valgrind_event_align.txt || die "failed"
+	test/test_eventalign.sh valgrind 2> valgrind_event_align.txt || die "failed"
 	echo ""
 	echo "____________________________________________________________________"