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Add tests for warnings in the body section
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@srbcheema1
srbcheema1 committed Apr 6, 2018
1 parent c0e3189 commit 7859b5c
Showing 1 changed file with 347 additions and 2 deletions.
349 changes: 347 additions & 2 deletions test/vcf/optional_policy_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,238 @@

namespace ebi
{


TEST_CASE("Record Position warnings", "[body position warnings]")
{
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::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;

SECTION("Non-zero position for non-telomeres")
{
CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { "XYZ", "1" } },
{ },
{ },
source})) );

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

TEST_CASE("Id warnings", "[body id warnings]")
{
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::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;

SECTION("Commas in ID column")
{
CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ "id1,id2" },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { "XYZ", "1" } },
{ },
{ },
source})),
vcf::IdBodyError*);
}
}

TEST_CASE("Record Reference Alternate matching warnings", "[body reference alternate matching warnings]")
{
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::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;

SECTION("Reference and alternate alleles share first nucleotide")
{
vcf::Record record1(
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { "XYZ", "1" } },
{ },
{ },
source);
record1.types = { vcf::RecordType::INDEL };

vcf::Record record2(
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"A",
{ "CA" },
1.0,
{ vcf::PASS },
{ { "XYZ", "1" } },
{ },
{ },
source);
record2.types = { vcf::RecordType::MNV };

vcf::Record record3(
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"AT",
{ "AC", "TAG" },
1.0,
{ vcf::PASS },
{ { "XYZ", "1" } },
{ },
{ },
source);
record3.types = { vcf::RecordType::INDEL };

CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, record1)) );

CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, record2)) );

CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, record3)),
vcf::ReferenceAlleleBodyError*);
}
}

TEST_CASE("Info predefined tags warnings", "[body info warnings]")
{
std::shared_ptr<vcf::Source> source{
Expand Down Expand Up @@ -65,7 +296,121 @@ namespace ebi

vcf::ValidateOptionalPolicy optional_policy;

SECTION("Confidence Interval Tags")
SECTION("IMPRECISE test")
{
source->meta_entries.emplace(vcf::INFO,
vcf::MetaEntry{
1,
vcf::INFO,
{
{ vcf::ID, vcf::IMPRECISE },
{ vcf::NUMBER, "0" },
{ vcf::TYPE, vcf::FLAG },
{ vcf::DESCRIPTION, "Imprecise structural variation" }
},
source
});

source->meta_entries.emplace(vcf::INFO,
vcf::MetaEntry{
1,
vcf::INFO,
{
{ vcf::ID, vcf::CIPOS },
{ vcf::NUMBER, "2" },
{ vcf::TYPE, vcf::INTEGER },
{ vcf::DESCRIPTION, "Confidence interval around POS for imprecise variants" }
},
source
});

source->meta_entries.emplace(vcf::INFO,
vcf::MetaEntry{
1,
vcf::INFO,
{
{ vcf::ID, vcf::CIEND },
{ vcf::NUMBER, "2" },
{ vcf::TYPE, vcf::INTEGER },
{ vcf::DESCRIPTION, "Confidence interval around END for imprecise variants" }
},
source
});

CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ "id123" },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { vcf::IMPRECISE, "0" } },
{ vcf::GT },
{ "1|0" },
source})) );

CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ "id123" },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { vcf::IMPRECISE, "1" }, { vcf::CIEND, "-2,1" } },
{ vcf::GT },
{ "1|0" },
source})) );

CHECK_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ "id123" },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { vcf::CIPOS, "-1,2" }, { vcf::IMPRECISE, "1" } },
{ vcf::GT },
{ "1|0" },
source})) );

CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ "id123" },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { vcf::CIEND, "-1,2"}, { vcf::IMPRECISE, "0" } },
{ vcf::GT },
{ "0|1" },
source})),
vcf::InfoBodyError*);

CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ "id123" },
"A",
{ "AC" },
1.0,
{ vcf::PASS },
{ { vcf::IMPRECISE, "0" }, { vcf::CIPOS, "-2,1" } },
{ vcf::GT },
{ "0|1" },
source})),
vcf::InfoBodyError*);
}

SECTION("Confidence Interval Tags")
{
std::vector<std::string> confidence_interval_tags = {
vcf::CICN,
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