diff --git a/src/bcftools/bcftools_norm/test.sh b/src/bcftools/bcftools_norm/test.sh index fd97cb59..254c7176 100644 --- a/src/bcftools/bcftools_norm/test.sh +++ b/src/bcftools/bcftools_norm/test.sh @@ -61,6 +61,7 @@ echo "> Run bcftools_norm" --output "normalized.vcf" \ --atomize \ --atom_overlaps "." \ + &> /dev/null # checks assert_file_exists "normalized.vcf" @@ -79,6 +80,7 @@ echo "> Run bcftools_norm with remove duplicates" --output "normalized.vcf" \ --atomize \ --remove_duplicates 'all' \ + &> /dev/null # checks assert_file_exists "normalized.vcf" @@ -98,6 +100,7 @@ echo "> Run bcftools_norm with check reference and fasta reference" --atomize \ --fasta_ref "../reference.fa" \ --check_ref "e" \ + &> /dev/null # checks assert_file_exists "normalized.vcf" @@ -116,6 +119,7 @@ echo "> Run bcftools_norm with multiallelics" --output "normalized.vcf" \ --multiallelics "-any" \ --old_rec_tag "wazzaaa" \ + &> /dev/null # checks assert_file_exists "normalized.vcf" @@ -134,6 +138,7 @@ echo "> Run bcftools_norm with regions" --output "normalized.vcf" \ --atomize \ --regions "1:752567-752722" \ + &> /dev/null # checks assert_file_exists "normalized.vcf" @@ -152,6 +157,7 @@ echo "> Run bcftools_norm with targets" --output "normalized.vcf" \ --atomize \ --targets "1:752567-752722" \ + &> /dev/null # checks assert_file_exists "normalized.vcf" @@ -170,6 +176,7 @@ echo "> Run bcftools_norm with regions overlap" --output "normalized.vcf" \ --atomize \ --regions_overlap "pos" \ + &> /dev/null # checks assert_file_exists "normalized.vcf" @@ -188,12 +195,13 @@ echo "> Run bcftools_norm with strict filter and targets overlap" --output "normalized.vcf" \ --atomize \ --strict_filter \ - --targets_overlap "pos" \ + --targets_overlap "1" \ + &> /dev/null # checks assert_file_exists "normalized.vcf" assert_file_not_empty "normalized.vcf" -assert_file_contains "normalized.vcf" "norm --atomize -s --targets-overlap pos -o normalized.vcf ../example.vcf" +assert_file_contains "normalized.vcf" "norm --atomize -s --targets-overlap 1 -o normalized.vcf ../example.vcf" echo "- test8 succeeded -" popd > /dev/null @@ -207,6 +215,7 @@ echo "> Run bcftools_norm with do not normalize" --output "normalized.vcf" \ --do_not_normalize \ --atomize \ + &> /dev/null # checks assert_file_exists "normalized.vcf"