From 527ffc353f6f82b309ef26d967f4a5efa9326285 Mon Sep 17 00:00:00 2001
From: Hasindu Gamaarachchi <hasindu2008@gmail.com>
Date: Sun, 2 Apr 2023 23:10:56 +1000
Subject: [PATCH] fix rsq

---
 scripts/test_extensive.sh | 19 +++++++++++++++++--
 scripts/test_rsq.sh       | 34 ++++++++++++++++++++--------------
 2 files changed, 37 insertions(+), 16 deletions(-)

diff --git a/scripts/test_extensive.sh b/scripts/test_extensive.sh
index 41a3433a..5f7b3842 100755
--- a/scripts/test_extensive.sh
+++ b/scripts/test_extensive.sh
@@ -132,9 +132,14 @@ test_suit1 () {
 
 
 	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"
-	scripts/test_lsk114.sh 2> lsk114.log || die "failed"
+	echo "____________________________________________________________________"
+	echo "methylation resquiggle"
+	scripts/test_rsq -f 2> r10_hg2_resquiggle.log || die "failed"
 
 	echo ""
 	echo "*********************************************************************"
@@ -162,6 +167,9 @@ test_suit1_cuda () {
 	echo "slow5"
 	scripts/test_slow5.sh 2> ecoli_slow5_cuda.log || die "failed"
 	echo "____________________________________________________________________"
+	echo "resquiggle"
+	scripts/test_rsq.sh 2> ecoli_resquiggle_cuda.log || die "failed"
+	echo "____________________________________________________________________"
 
 	echo ""
 	echo "*********************************************************************"
@@ -191,12 +199,19 @@ test_suit1_cuda () {
 	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"
 	echo "____________________________________________________________________"
+	echo "resquiggle"
+	scripts/test_rsq.sh -e 2> rna_resquiggle_cuda.log || die "failed"
 
 
 	echo "************************Doing R10 HG2 tests*****************************"
-	scripts/test_lsk114.sh 2> lsk114_cuda.log || die "failed"
+	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.log || die "failed"
+	echo "____________________________________________________________________"
+	echo "resquiggle"
+	scripts/test_rsq -f 2> r10_hg2_resquiggle.log || die "failed"
 
 	echo ""
 	echo "*********************************************************************"
diff --git a/scripts/test_rsq.sh b/scripts/test_rsq.sh
index 95deaf15..013c2840 100755
--- a/scripts/test_rsq.sh
+++ b/scripts/test_rsq.sh
@@ -45,9 +45,9 @@ download_test_set() {
 
 
 handle_tests() {
-	numfailed=$(wc -l < ${testdir}/floatdiff.txt)
-	numcases=$(wc -l < ${testdir}/meth_float.txt)
-	numres=$(wc -l < ${testdir}/result_float.txt)
+	numfailed=$(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"
@@ -58,17 +58,23 @@ handle_tests() {
 
 execute_test() {
 
-	ARCH=$(uname -m)
-	if [ $ARCH != "aarm64" ]; then
-		if [ $testdir = test/chr22_meth_example ]; then
-			echo "Diff not yet implemented for chr22_meth_example"
-		elif [ $testdir = test/ecoli_2kb_region ]; then
-			diff -q ${testdir}/result.txt ${testdir}_big_testresults/resquiggle.tsv || die "Validation of tsv failed"
-			diff -q ${testdir}/result2.txt ${testdir}_big_testresults/resquiggle.paf || die "Validation of paf failed"
-		elif [ $testdir = test/rna ]; then
-			diff -q ${testdir}/result.txt ${testdir}/resquiggle.tsv || die "Validation of tsv failed"
-			diff -q ${testdir}/result2.txt ${testdir}/resquiggle.paf || die "Validation of paf failed"
-		fi
+
+	if [ $testdir = test/chr22_meth_example ]; then
+		echo "Diff not yet implemented for chr22_meth_example"
+	elif [ $testdir = test/ecoli_2kb_region ]; then
+		ORIG=${testdir}_big_testresults/resquiggle.tsv
+		RES=${testdir}/result.txt
+		diff -y --suppress-common-lines ${ORIG} ${RES} > ${testdir}/diff.txt || handle_tests
+		ORIG=${testdir}_big_testresults/resquiggle.paf
+		RES=${testdir}/result2.txt
+		diff -y --suppress-common-lines ${ORIG} ${RES} > ${testdir}/diff.txt || handle_tests
+	else
+		ORIG=${testdir}/resquiggle.tsv
+		RES=${testdir}/result.txt
+		diff -y --suppress-common-lines ${ORIG} ${RES} > ${testdir}/diff.txt || handle_tests
+		ORIG=${testdir}/resquiggle.paf
+		RES=${testdir}/result2.txt
+		diff -y --suppress-common-lines ${ORIG} ${RES} > ${testdir}/diff.txt || handle_tests
 	fi