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@cli
Feature: Command-line interface (CLI)
bio-vcf has a powerful command line interface. Here we regression test features.
Scenario: Test the info filter using dp
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf -i --filter 'r.info.dp>100'"
Then I expect the named output to match the named output "r.info.dp"
Scenario: Test the info filter using dp and threads
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf -i --num-threads 4 --filter 'r.info.dp>2'"
Then I expect the named output to match the named output "thread4" in under 30 seconds
Scenario: Test the info filter using dp and threads with lines
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf -i --num-threads 4 --thread-lines 4 --filter 'r.info.dp>2'"
Then I expect the named output to match the named output "thread4_4" in under 30 seconds
Scenario: Test the sample filter using dp
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf -i --sfilter 's.dp>20'"
Then I expect the named output to match the named output "s.dp"
Scenario: Test the include sample filter using dp
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf -i --ifilter 's.dp>100' --seval s.dp"
Then I expect the named output to match the named output "ifilter_s.dp"
Scenario: Test the info eval using dp
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf -i --eval 'r.info.dp'"
Then I expect the named output to match the named output "eval_r.info.dp"
Scenario: Test the sample eval using dp
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf -i --seval 's.dp'"
Then I expect the named output to match the named output "seval_s.dp"
Scenario: Test the sample filter + eval using dp
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf -i --sfilter 's.dp>10' --seval 's.dp'"
Then I expect the named output to match the named output "sfilter_seval_s.dp"
Scenario: Rewrite an info field
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf --rewrite rec.info[\'sample\']=\'XXXXX\'"
Then I expect the named output to match the named output "rewrite.info.sample"
Scenario: Test eval-once
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf --eval-once header.meta[\'GATKCommandLine\']"
Then I expect the named output to match the named output "eval_once"
Scenario: Test JSON output with header meta data
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf --template template/vcf2json_full_header.erb"
Then I expect the named output to match the named output "vcf2json_full_header"
Scenario: Test JSON output with header meta data and query samples
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf --template template/vcf2json_use_meta.erb"
Then I expect the named output to match the named output "vcf2json_use_meta"
Scenario: Test deadlock on failed filter with threads
Given I have input file(s) named "test/data/input/multisample.vcf"
When I execute "./bin/bio-vcf -q --timeout 4 --num-threads 4 --thread-lines 4 --filter 't.info.dp>2'"
Then I expect an error and the named output to match the named output "thread4_4_failed_filter" in under 30 seconds
Scenario: Test VCF with no records
Given I have input file(s) named "test/data/input/empty.vcf"
When I execute "./bin/bio-vcf --timeout=5"
Then I expect no errors
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