From 1946874ff917d5ce9602194befa62bd9ca3d7035 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Thu, 29 Aug 2024 15:19:12 +0200
Subject: [PATCH] add template for tests

---
 src/bcftools/bcftools_concat/script.sh |  5 +-
 src/bcftools/bcftools_concat/test.sh   | 70 ++++++++++++++++++++++++++
 2 files changed, 74 insertions(+), 1 deletion(-)

diff --git a/src/bcftools/bcftools_concat/script.sh b/src/bcftools/bcftools_concat/script.sh
index 6cd9d4db..d77e0615 100644
--- a/src/bcftools/bcftools_concat/script.sh
+++ b/src/bcftools/bcftools_concat/script.sh
@@ -23,6 +23,9 @@ for par in ${unset_if_false[@]}; do
     [[ "$test_val" == "false" ]] && unset $par
 done
 
+# Create input array 
+IFS=";" read -ra input <<< $par_input
+
 # Execute bcftools concat with the provided arguments
 bcftools concat \
     ${par_allow_overlaps:+-a} \
@@ -43,4 +46,4 @@ bcftools concat \
     ${par_threads:+--threads "$par_threads"} \
     ${par_verbose:+-v "$par_verbose"} \
     -o $par_output \
-    $par_input
\ No newline at end of file
+    ${input[@]} \
\ No newline at end of file
diff --git a/src/bcftools/bcftools_concat/test.sh b/src/bcftools/bcftools_concat/test.sh
index e69de29b..e07b8250 100644
--- a/src/bcftools/bcftools_concat/test.sh
+++ b/src/bcftools/bcftools_concat/test.sh
@@ -0,0 +1,70 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# Exit on error
+set -eo pipefail
+
+#test_data="$meta_resources_dir/test_data"
+
+#############################################
+# helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+assert_file_not_empty() {
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
+}
+assert_file_contains() {
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+assert_identical_content() {
+  diff -a "$2" "$1" \
+    || (echo "Files are not identical!" && exit 1)
+}
+#############################################
+
+# Create directories for tests
+echo "Creating Test Data..."
+TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+
+# Create test data
+cat <<EOF > "$TMPDIR/example.vcf"
+##fileformat=VCFv4.1
+##contig=<ID=1,length=249250621,assembly=b37>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE1
+1	752567	llama	G	C,A	.	.	.	.	1/2
+1	752722	.	G	A,AAA	.	.	.	.	./.
+EOF
+
+bgzip -c $TMPDIR/example.vcf > $TMPDIR/example.vcf.gz
+tabix -p vcf $TMPDIR/example.vcf.gz
+
+# Test 1: Remove ID annotations
+mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
+
+echo "> Run bcftools_norm"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "normalized.vcf" \
+  --atomize \
+  --atom_overlaps "." \
+  &> /dev/null
+
+# checks
+assert_file_exists "normalized.vcf"
+assert_file_not_empty "normalized.vcf"
+assert_file_contains "normalized.vcf" "bcftools_normCommand=norm --atomize --atom-overlaps . -o normalized.vcf ../example.vcf"
+echo "- test1 succeeded -"
+
+popd > /dev/null
+
+echo "---- All tests succeeded! ----"
+exit 0
+
+