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Test cases for the NoMetaDefinitionError warning #127

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Test cases for the NoMetaDefinitionError warning #127

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b6fa109
Added test cases for missing meta-data of INFO and FORMAT
srbcheema1 Mar 16, 2018
1dd5910
Added test cases for missing meta-data of filter and alternate allele
srbcheema1 Mar 16, 2018
49624f6
Added test cases for missing meta-data of reference and contig
srbcheema1 Mar 16, 2018
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348 changes: 348 additions & 0 deletions test/vcf/optional_policy_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -389,4 +389,352 @@ namespace ebi
vcf::AlternateAllelesBodyError*);
}
}

TEST_CASE("Meta-data warnings", "[warnings]")
{
SECTION("Reference not in meta section")
{
std::shared_ptr<vcf::Source> source{
new vcf::Source{
"Example VCF source",
vcf::InputFormat::VCF_FILE_VCF | vcf::InputFormat::VCF_FILE_BGZIP,
vcf::Version::v43}};

vcf::ParsingState parsing_state{source};

vcf::ValidateOptionalPolicy optional_policy;

CHECK_THROWS_AS( (optional_policy.optional_check_meta_section(parsing_state)), vcf::MetaSectionError*);
}

SECTION("Contig not in meta section")
{
std::shared_ptr<vcf::Source> source{
new vcf::Source{
"Example VCF source",
vcf::InputFormat::VCF_FILE_VCF | vcf::InputFormat::VCF_FILE_BGZIP,
vcf::Version::v43}};

source->meta_entries.emplace(vcf::REFERENCE,
vcf::MetaEntry{
1,
vcf::REFERENCE,
"file",
source
});

source->meta_entries.emplace(vcf::CONTIG,
vcf::MetaEntry{
1,
vcf::CONTIG,
{ { vcf::ID, "chr1" } },
source
});

vcf::ParsingState parsing_state{source};

vcf::ValidateOptionalPolicy optional_policy;

CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { vcf::MISSING_VALUE, "" } },
{ },
{ },
source})) );

CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr2",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { vcf::MISSING_VALUE, "" } },
{ },
{ },
source})),
vcf::NoMetaDefinitionError*);
}

SECTION("Alternate Allele not in meta section")
{
std::shared_ptr<vcf::Source> source{
new vcf::Source{
"Example VCF source",
vcf::InputFormat::VCF_FILE_VCF | vcf::InputFormat::VCF_FILE_BGZIP,
vcf::Version::v43}};

source->meta_entries.emplace(vcf::REFERENCE,
vcf::MetaEntry{
1,
vcf::REFERENCE,
"file",
source
});

source->meta_entries.emplace(vcf::CONTIG,
vcf::MetaEntry{
1,
vcf::CONTIG,
{ { vcf::ID, "chr1" } },
source
});

source->meta_entries.emplace(vcf::ALT,
vcf::MetaEntry{
1,
vcf::ALT,
{
{ vcf::ID, "DEL" },
{ vcf::DESCRIPTION, "Random alt tag" }
},
source
});

vcf::ParsingState parsing_state{source};

vcf::ValidateOptionalPolicy optional_policy;

CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { vcf::MISSING_VALUE, "" } },
{ },
{ },
source})) );

CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "<DEL>" },
1.0,
{ vcf::PASS },
{ { vcf::MISSING_VALUE, "" } },
{ },
{ },
source})) );

CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "<INS>" },
1.0,
{ vcf::PASS },
{ { vcf::MISSING_VALUE, "" } },
{ },
{ },
source})),
vcf::NoMetaDefinitionError*);
}

SECTION("FILTER not in meta section")
{
std::shared_ptr<vcf::Source> source{
new vcf::Source{
"Example VCF source",
vcf::InputFormat::VCF_FILE_VCF | vcf::InputFormat::VCF_FILE_BGZIP,
vcf::Version::v43}};

source->meta_entries.emplace(vcf::REFERENCE,
vcf::MetaEntry{
1,
vcf::REFERENCE,
"file",
source
});

source->meta_entries.emplace(vcf::CONTIG,
vcf::MetaEntry{
1,
vcf::CONTIG,
{ { vcf::ID, "chr1" } },
source
});

vcf::ParsingState parsing_state{source};

vcf::ValidateOptionalPolicy optional_policy;

CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { vcf::MISSING_VALUE, "" } },
{ },
{ },
source})) );

CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "AC" },
1.0,
{ vcf::MISSING_VALUE },
{ { vcf::MISSING_VALUE, "" } },
{ },
{ },
source})) );

CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "AC" },
1.0,
{ "q10" },
{ { vcf::MISSING_VALUE, "" } },
{ },
{ },
source})),
vcf::NoMetaDefinitionError*);
}

SECTION("INFO not in meta section")
{
std::shared_ptr<vcf::Source> source{
new vcf::Source{
"Example VCF source",
vcf::InputFormat::VCF_FILE_VCF | vcf::InputFormat::VCF_FILE_BGZIP,
vcf::Version::v43}};

source->meta_entries.emplace(vcf::REFERENCE,
vcf::MetaEntry{
1,
vcf::REFERENCE,
"file",
source
});

source->meta_entries.emplace(vcf::CONTIG,
vcf::MetaEntry{
1,
vcf::CONTIG,
{ { vcf::ID, "chr1" } },
source
});

vcf::ParsingState parsing_state{source};

vcf::ValidateOptionalPolicy optional_policy;

CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { vcf::MISSING_VALUE, "" } },
{ },
{ },
source})) );

CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { "ABC", "1" } },
{ },
{ },
source})),
vcf::NoMetaDefinitionError*);
}

SECTION("FORMAT not in meta section")
{
std::shared_ptr<vcf::Source> source{
new vcf::Source{
"Example VCF source",
vcf::InputFormat::VCF_FILE_VCF | vcf::InputFormat::VCF_FILE_BGZIP,
vcf::Version::v43,
{},
{ "Sample1" }}};

source->meta_entries.emplace(vcf::REFERENCE,
vcf::MetaEntry{
1,
vcf::REFERENCE,
"file",
source
});

source->meta_entries.emplace(vcf::CONTIG,
vcf::MetaEntry{
1,
vcf::CONTIG,
{ { vcf::ID, "chr1" } },
source
});

source->meta_entries.emplace(vcf::INFO,
vcf::MetaEntry{
1,
vcf::INFO,
{
{ vcf::ID, "XYZ" },
{ vcf::NUMBER, "1" },
{ vcf::TYPE, vcf::INTEGER },
{ vcf::DESCRIPTION, "Random info tag" }
},
source
});

vcf::ParsingState parsing_state{source};

vcf::ValidateOptionalPolicy optional_policy;

CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { "XYZ", "1" } },
{ vcf::GT },
{ "0|1" },
source})),
vcf::NoMetaDefinitionError*);
}
}
}