adding more tests

src/bcftools/bcftools_concat/config.vsh.yaml

@@ -30,8 +30,12 @@ argument_groups:
         alternatives: -i
         type: file
         multiple: true
-        description: Input VCF/BCF file.
-        required: true
+        description: Input VCF/BCF files to concatenate.
+
+      - name: --file_list
+        alternatives: -f
+        type: file
+        description: Read the list of VCF/BCF files from a file, one file name per line.
 
   - name: Outputs
     arguments:
@@ -60,14 +64,9 @@ argument_groups:
       - name: --remove_duplicates
         alternatives: -d
         type: string
-        choices: ['snps', 'indels', 'both', 'all', 'exact']
+        choices: ['snps', 'indels', 'both', 'all', 'exact', 'none']
         description: |
           Output duplicate records present in multiple files only once: <snps|indels|both|all|exact>.
-      
-      - name: --file_list
-        alternatives: -f
-        type: file
-        description: Read the list of files from a file.
               
       - name: --ligate
         alternatives: -l

src/bcftools/bcftools_concat/script.sh

@@ -23,6 +23,12 @@ for par in ${unset_if_false[@]}; do
     [[ "$test_val" == "false" ]] && unset $par
 done
 
+# Check to see whether the par_input or the par_file_list is set
+if [[ -z "${par_input}" && -z "${par_file_list}" ]]; then
+    echo "Error: One of the parameters '--input' or '--file_list' must be used."
+    exit 1
+fi
+
 # Create input array 
 IFS=";" read -ra input <<< $par_input
 
@@ -31,7 +37,6 @@ bcftools concat \
     ${par_allow_overlaps:+-a} \
     ${par_compact_PS:+-c} \
     ${par_remove_duplicates:+-d "$par_remove_duplicates"} \
-    ${par_file_list:+-f "$par_file_list"} \
     ${par_ligate:+-l} \
     ${par_ligate_force:+--ligate-force} \
     ${par_ligate_warn:+--ligate-warn} \
@@ -46,4 +51,5 @@ bcftools concat \
     ${meta_cpus:+--threads "$meta_cpus"} \
     ${par_verbose:+-v "$par_verbose"} \
     -o $par_output \
+    ${par_file_list:+-f "$par_file_list"} \
     ${input[@]} \

src/bcftools/bcftools_concat/test.sh

@@ -39,7 +39,7 @@ cat <<EOF > "$TMPDIR/example.vcf"
 ##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	.	.	.	.	./.
+1	752752	.	G	A,AAA	.	.	.	.	./.
 EOF
 
 bgzip -c $TMPDIR/example.vcf > $TMPDIR/example.vcf.gz
@@ -53,6 +53,14 @@ cat <<EOF > "$TMPDIR/example_2.vcf"
 1	752739	.	G	A,AAA	.	.	.	.	./.
 EOF
 
+bgzip -c $TMPDIR/example_2.vcf > $TMPDIR/example_2.vcf.gz
+tabix -p vcf $TMPDIR/example_2.vcf.gz
+
+cat <<EOF > "$TMPDIR/file_list.txt"
+$TMPDIR/example.vcf.gz
+$TMPDIR/example_2.vcf.gz
+EOF
+
 # Test 1: Default test
 mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
 
@@ -72,6 +80,66 @@ echo "- test1 succeeded -"
 
 popd > /dev/null
 
+# Test 2: Allow overlaps, compact PS and remove duplicates
+mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null
+
+echo "> Run bcftools_concat test with allow overlaps, and remove duplicates"
+"$meta_executable" \
+  --input "../example.vcf.gz" \
+  --input "../example_2.vcf.gz" \
+  --output "concatenated.vcf" \
+  --allow_overlaps \
+  --remove_duplicates 'none' \
+#  &> /dev/null
+
+# checks
+assert_file_exists "concatenated.vcf"
+assert_file_not_empty "concatenated.vcf"
+assert_file_contains "concatenated.vcf" "concat -a -d none -o concatenated.vcf ../example.vcf.gz ../example_2.vcf.gz"  
+echo "- test2 succeeded -"
+
+popd > /dev/null
+
+
+# Test 3: Ligate, ligate force and ligate warn
+mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null
+
+echo "> Run bcftools_concat test with ligate, ligate force and ligate warn"
+"$meta_executable" \
+  --input "../example.vcf.gz" \
+  --input "../example_2.vcf.gz" \
+  --output "concatenated.vcf" \
+  --ligate \
+  --compact_PS \
+#  &> /dev/null
+
+
+# checks
+assert_file_exists "concatenated.vcf"
+assert_file_not_empty "concatenated.vcf"
+assert_file_contains "concatenated.vcf" "concat -c -l -o concatenated.vcf ../example.vcf.gz ../example_2.vcf.gz"
+echo "- test3 succeeded -"
+
+popd > /dev/null
+
+# Test 4: file list with ligate force and ligate warn
+mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null
+
+echo "> Run bcftools_concat test with file list, ligate force and ligate warn"
+"$meta_executable" \
+  --file_list "../file_list.txt" \
+  --output "concatenated.vcf" \
+  --ligate_force \
+#  &> /dev/null
+
+# checks
+assert_file_exists "concatenated.vcf"
+assert_file_not_empty "concatenated.vcf"
+assert_file_contains "concatenated.vcf" "concat --ligate-force -o concatenated.vcf -f ../file_list.txt"
+echo "- test4 succeeded -"
+
+popd > /dev/null
+
 echo "---- All tests succeeded! ----"
 exit 0