adding more tests

src/bcftools/bcftools_stats/config.vsh.yaml

@@ -90,7 +90,7 @@ argument_groups:
           The file is BGZF-compressed and indexed with tabix
           e.g. 
             tabix -s1 -b2 -e3 file.gz
-            
+
       - name: --apply_filters
         alternatives: --f
         type: string
@@ -174,15 +174,14 @@ argument_groups:
         description: | 
           Produce verbose per-site and per-sample output.
 
-
 resources:
   - type: bash_script
     path: script.sh
 
 test_resources:
   - type: bash_script
     path: test.sh
-  # - path: test_data
+  - path: test_data
 
 engines:
   - type: docker
@@ -193,6 +192,9 @@ engines:
       - type: docker
         run: |
           echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt
+    test_setup:  
+      - type: apt  
+        packages: [tabix, samtools]
 
 runners:
   - type: executable

src/bcftools/bcftools_stats/test.sh

@@ -69,6 +69,27 @@ cat <<EOF > "$TMPDIR/example.vcf"
 20	1234567	microsat1	G	GA,GAC	50	PASS	NS=3;DP=9;AA=G;AN=6;AC=3,1	GT:GQ:DP	0/1:.:4	0/2:17:2	1/1:40:3
 EOF
 
+cat <<EOF > "$TMPDIR/exons.bed"
+chr19	12345	12567
+chr20	23456	23789
+EOF
+
+# Compressing and indexing the exons file
+bgzip -c $TMPDIR/exons.bed > $TMPDIR/exons.bed.gz
+tabix -s1 -b2 -e3 $TMPDIR/exons.bed.gz
+
+# Create test data
+cat <<EOF > "$TMPDIR/reference.fasta"
+>seq1
+ATGCGTACGTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGC
+>seq2
+CGTAGCTAGCTAGGCTAGCTGATCGATCGTAGCTAGCTAGC
+>seq3
+TGCATGCTAGCTAGCTGATCGTAGCTAGCTAGCTAGCTAGC
+EOF
+
+# Index the fasta reference
+#samtools faidx $TMPDIR/reference.fasta
 
 # Test 1: Default Use
 mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
@@ -141,48 +162,42 @@ echo "- test4 succeeded -"
 
 popd > /dev/null
 
-# # Test 5: Exons, Apply Filters, Fasta Reference
-# mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null
-
-# echo "> Run bcftools_stats on VCF file with exons, apply filters, and fasta reference"
-# "$meta_executable" \
-#   --input "../example.vcf" \
-#   --output "stats.txt" \
-#   --exons "exons.bed" \
-#   --apply_filters "PASS" \
-#   --fasta_reference "reference.fasta" \
+# Test 5: Exons, Apply Filters, Fasta Reference
+mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null
 
-# echo 
-# cat stats.txt
-# echo
-# exit 0
+echo "> Run bcftools_stats on VCF file with exons, apply filters, and fasta reference"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "stats.txt" \
+  --exons "../exons.bed.gz" \
+  --apply_filters "PASS" \
+  #--fasta_reference "../reference.fasta.fai" \
 
-# # checks
-# assert_file_exists "stats.txt"
-# assert_file_not_empty "stats.txt"
-# assert_file_contains "stats.txt" "number of records:	8"
-# echo "- test5 succeeded -"
+# checks
+assert_file_exists "stats.txt"
+assert_file_not_empty "stats.txt"
+assert_file_contains "stats.txt" "bcftools stats  -E ../exons.bed.gz -f PASS ../example.vcf"
+echo "- test5 succeeded -"
 
-# popd > /dev/null
+popd > /dev/null
 
-# # Test 6: Include, Regions, Regions File
-# mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null
+# Test 6: Include, Regions, Regions File
+mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null
 
-# echo "> Run bcftools_stats on VCF file with include, regions, and regions file"
-# "$meta_executable" \
-#   --input "../example.vcf" \
-#   --output "stats.txt" \
-#   --include "PASS" \
-#   --regions "20:1000000-2000000" \
-#   --regions_file "regions.bed" \
+echo "> Run bcftools_stats on VCF file with include, regions, and regions file"
+"$meta_executable" \
+  --input "../example.vcf" \
+  --output "stats.txt" \
+  --include "GT='mis'" \
+  --regions "20" \
 
-# # checks
-# assert_file_exists "stats.txt"
-# assert_file_not_empty "stats.txt"
-# assert_file_contains "stats.txt" "number of records:	8"
-# echo "- test6 succeeded -"
+# checks
+assert_file_exists "stats.txt"
+assert_file_not_empty "stats.txt"
+assert_file_contains "stats.txt" "number of records:	8"
+echo "- test6 succeeded -"
 
-# popd > /dev/null
+popd > /dev/null
 
 # # Test 7: Regions Overlap, Samples, Samples File
 # mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null