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Tests for warnings in the body section #121

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Tests for warnings in the body section #121

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7859b5c
Add tests for warnings in the body section
srbcheema1 Mar 12, 2018
4a24173
Updated ref alt test cases to use constructor
srbcheema1 Mar 15, 2018
ce18628
Change tag message to 'warnings'
srbcheema1 Mar 15, 2018
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346 changes: 341 additions & 5 deletions test/vcf/optional_policy_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,230 @@

namespace ebi
{

TEST_CASE("Info predefined tags warnings", "[body info warnings]")

TEST_CASE("Record Position warnings", "[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", "[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", "[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")
{
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_NOTHROW( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"GT",
{ "AC" },
1.0,
{ vcf::PASS },
{ { "XYZ", "1" } },
{ },
{ },
source})) );

CHECK_THROWS_AS( (optional_policy.optional_check_body_entry(parsing_state, vcf::Record{
1,
"chr1",
123456,
{ vcf::MISSING_VALUE },
"AT",
{ "AC", "TAG" },
1.0,
{ vcf::PASS },
{ { "XYZ", "1" } },
{ },
{ },
source})),
vcf::ReferenceAlleleBodyError*);
}
}

TEST_CASE("Info predefined tags warnings", "[warnings]")
{
std::shared_ptr<vcf::Source> source{
new vcf::Source{
Expand Down Expand Up @@ -65,9 +287,123 @@ 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 = {
std::vector<std::string> confidence_interval_tags = {
vcf::CICN,
vcf::CICNADJ,
vcf::CIEND,
Expand Down Expand Up @@ -182,7 +518,7 @@ namespace ebi
}
}

TEST_CASE("Alternate allele warnings", "[body alt warnings]")
TEST_CASE("Alternate allele warnings", "[warnings]")
{
std::vector<std::shared_ptr<vcf::Source>> sources = {
std::shared_ptr<vcf::Source>{new vcf::Source{
Expand Down