diff --git a/inc/vcf/file_structure.hpp b/inc/vcf/file_structure.hpp index ff4faf3a1..66b2ce67b 100644 --- a/inc/vcf/file_structure.hpp +++ b/inc/vcf/file_structure.hpp @@ -27,6 +27,25 @@ namespace opencb typedef std::multimap::iterator meta_iterator; + enum InputFormat + { + VCF_FILE_VCF = 0x01, + VCF_FILE_GVCF = 0x02, + VCF_FILE_GZIP = 0x04, + VCF_FILE_BGZIP = 0x08, + VCF_FILE_BCF = 0x10, + }; + + enum class RecordType + { + SNV, + MNV, + INDEL, + STRUCTURAL, + STRUCTURAL_BREAKEND, + NO_VARIATION + }; + struct MetaEntry { @@ -59,15 +78,6 @@ namespace opencb void check_value(); }; - enum InputFormat - { - VCF_FILE_VCF = 0x01, - VCF_FILE_GVCF = 0x02, - VCF_FILE_GZIP = 0x04, - VCF_FILE_BGZIP = 0x08, - VCF_FILE_BCF = 0x10, - }; - struct Source { std::string name; /**< Name of the source to interact with (file, stdin...) */ @@ -92,7 +102,8 @@ namespace opencb std::string reference_allele; std::vector alternate_alleles; - + std::vector types; + float quality; std::vector filters; std::map info; @@ -120,6 +131,9 @@ namespace opencb bool operator!=(Record const &) const; private: + + void set_types(); + /** * Checks that chromosome does not contain colons or white-spaces * @@ -149,7 +163,7 @@ namespace opencb * * @throw std::invalid_argument */ - void check_alternate_allele_structure(std::string const & alternate) const; + void check_alternate_allele_structure(std::string const & alternate, RecordType type) const; /** * Checks that alternates of the form are described in the meta section diff --git a/inc/vcf/validator.hpp b/inc/vcf/validator.hpp index 8a107b80b..a63b50a37 100644 --- a/inc/vcf/validator.hpp +++ b/inc/vcf/validator.hpp @@ -235,6 +235,8 @@ namespace opencb private: void check_body_entry_ploidy(ParsingState & state, Record & record); + void check_body_entry_reference_alternate_matching(ParsingState & state, Record & record); + void check_contig_meta(ParsingState & state, Record & record) const; void check_alternate_allele_meta(ParsingState & state, Record & record) const; void check_filter_meta(ParsingState & state, Record & record) const; diff --git a/src/vcf/record.cpp b/src/vcf/record.cpp index 3923fe85e..e74f0c197 100644 --- a/src/vcf/record.cpp +++ b/src/vcf/record.cpp @@ -22,6 +22,7 @@ namespace opencb ids{ids}, reference_allele{reference_allele}, alternate_alleles{alternate_alleles}, + types{}, quality{quality}, filters{filters}, info{info}, @@ -29,6 +30,7 @@ namespace opencb samples{samples}, source{source} { + set_types(); check_chromosome(); check_ids(); check_alternate_alleles(); @@ -58,6 +60,25 @@ namespace opencb return !(*this == other); } + void Record::set_types() + { + for (int i = 0; i < alternate_alleles.size(); ++i) { + auto & alternate = alternate_alleles[i]; + if (alternate == ".") { + types.push_back(RecordType::NO_VARIATION); + } else if (alternate[0] == '<') { + types.push_back(RecordType::STRUCTURAL); + } else if (std::count(alternate.begin(), alternate.end(), '[') == 2 || + std::count(alternate.begin(), alternate.end(), ']') == 2) { + types.push_back(RecordType::STRUCTURAL_BREAKEND); + } else if (alternate.size() != reference_allele.size()) { + types.push_back(RecordType::INDEL); + } else { + types.push_back(alternate.size() == 1 ? RecordType::SNV : RecordType::MNV); + } + } + } + void Record::check_chromosome() const { if (chromosome.find(':') != std::string::npos) { @@ -75,7 +96,7 @@ namespace opencb } for (auto & id : ids) { - if (find_if(id.begin(), id.end(), [](char c) { return c == ' ' || c == ';'; }) != id.end()) { + if (std::find_if(id.begin(), id.end(), [](char c) { return c == ' ' || c == ';'; }) != id.end()) { throw std::invalid_argument("ID must not contain semicolons or whitespaces"); } } @@ -86,12 +107,15 @@ namespace opencb static boost::regex square_brackets_regex("<([a-zA-Z0-9:_]+)>"); boost::cmatch pieces_match; - for (auto & alternate : alternate_alleles) { + for (size_t i = 0 ; i < alternate_alleles.size(); ++i) { + auto & alternate = alternate_alleles[i]; + auto & type = types[i]; + // Check alternate allele structure against the reference - check_alternate_allele_structure(alternate); + check_alternate_allele_structure(alternate, type); // Check that an alternate of the form begins with DEL, INS, DUP, INV or CNV - if (alternate[0] == '<' && regex_match(alternate.c_str(), pieces_match, square_brackets_regex)) { + if (alternate[0] == '<' && boost::regex_match(alternate.c_str(), pieces_match, square_brackets_regex)) { std::string alt_id = pieces_match[1]; if (!boost::starts_with(alt_id, "DEL") && !boost::starts_with(alt_id, "INS") && @@ -105,22 +129,28 @@ namespace opencb } - void Record::check_alternate_allele_structure(std::string const & alternate) const + void Record::check_alternate_allele_structure(std::string const & alternate, RecordType type) const { - if (alternate == ".") { - if (alternate_alleles.size() > 1) { - throw std::invalid_argument("The no-alternate alleles symbol (dot) can not be combined with others"); - } - } else if (alternate[0] == '<') { - return; // Custom ALTs can't be checked against the reference - } else if (std::count(alternate.begin(), alternate.end(), '[') == 2 || - std::count(alternate.begin(), alternate.end(), ']') == 2) { - return; // Break-ends can't be checked against the reference - } else if (alternate[0] != reference_allele[0] && alternate.size() != reference_allele.size()) { - throw std::invalid_argument("Reference and alternate alleles must share the first nucleotide"); - } else if (alternate == reference_allele) { - throw std::invalid_argument("Reference and alternate alleles must not be the same"); + switch (type) { + case RecordType::NO_VARIATION: + if (alternate_alleles.size() > 1) { + throw std::invalid_argument("The no-alternate alleles symbol (dot) can not be combined with others"); + } + break; + case RecordType::SNV: + case RecordType::MNV: + if (alternate == reference_allele) { + throw std::invalid_argument("Reference and alternate alleles must not be the same"); + } + case RecordType::INDEL: + // Nothing to check + break; + case RecordType::STRUCTURAL: + case RecordType::STRUCTURAL_BREAKEND: + // Custom ALTs (STRUCTURAL) and break-ends (STRUCTURAL_BREAKEND) can't be checked against the reference + break; } + } void Record::check_quality() const diff --git a/src/vcf/validate_optional_policy.cpp b/src/vcf/validate_optional_policy.cpp index 081ffff29..5a0b21d14 100644 --- a/src/vcf/validate_optional_policy.cpp +++ b/src/vcf/validate_optional_policy.cpp @@ -19,6 +19,9 @@ namespace opencb // All samples should have the same ploidy check_body_entry_ploidy(state, record); + // Reference and alternate alleles in indels should share the first nucleotide + check_body_entry_reference_alternate_matching(state, record); + /* * Once some meta-data is marked as in/correct there is no need again, so all the following have been * optimised using a map for correctly defined meta-data and another one for incorrectly defined. @@ -79,6 +82,18 @@ namespace opencb } } + void ValidateOptionalPolicy::check_body_entry_reference_alternate_matching(ParsingState & state, Record & record) + { + for (size_t i = 0; i < record.alternate_alleles.size(); ++i) { + auto & alternate = record.alternate_alleles[i]; + auto type = record.types[i]; + + if (type == RecordType::INDEL && alternate[0] != record.reference_allele[0]) { + throw ParsingWarning("Reference and alternate alleles do not share the first nucleotide"); + } + } + } + void ValidateOptionalPolicy::check_contig_meta(ParsingState & state, Record & record) const { // The associated 'contig' meta entry should exist (notify only once) @@ -107,7 +122,7 @@ namespace opencb for (auto & alternate : record.alternate_alleles) { // Check alternate ID is present in meta-entry (only applies to the form ) - if (alternate[0] == '<' && regex_match(alternate.c_str(), pieces_match, square_brackets_regex)) { + if (alternate[0] == '<' && boost::regex_match(alternate.c_str(), pieces_match, square_brackets_regex)) { std::string alt_id = pieces_match[1]; if (state.is_bad_defined_meta("ALT", alt_id) || diff --git a/test/invalid_context.vcf b/test/invalid_context.vcf index aa165c190..b3bd94adb 100644 --- a/test/invalid_context.vcf +++ b/test/invalid_context.vcf 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1|1:2.000:-2.65,-0.44,-0.20 1|1:1.700:-0.48,-0.48,-0.48 1|1:1.950:-2.49,-0.44,-0.20 1|1:1.700:-0.48,-0.48,-0.48 1|1:2.000:-3.00,-0.45,-0.19 1|1:2.000:-5.00,-0.86,-0.06 1|1:1.750:-0.48,-0.48,-0.48 1|1:1.700:-0.48,-0.48,-0.48 1|1:1.950:-0.48,-0.48,-0.48 1|1:1.800:-0.48,-0.48,-0.48 1|1:2.000:-2.69,-0.45,-0.19 1|1:1.900:-0.48,-0.48,-0.48 1|1:2.000:-2.70,-0.45,-0.19 1|1:1.700:-0.41,-0.45,-0.59 1|1:1.800:-2.62,-0.45,-0.19 1|1:1.650:-0.48,-0.48,-0.48 1|1:1.950:-2.01,-0.41,-0.22 0|1:0.800:-0.48,-0.48,-0.48 1|1:2.000:-5.00,-1.08,-0.04 1|1:1.950:-5.00,-0.77,-0.08 1|1:1.400:-0.48,-0.48,-0.48 1|1:2.000:-4.70,-0.65,-0.11 1|0:1.350:-0.48,-0.48,-0.48 1|1:1.750:-0.48,-0.48,-0.48 1|1:2.000:-5.00,-0.86,-0.07 1|1:1.950:-5.00,-0.84,-0.07 1|1:1.800:-0.477139,-0.477113,-0.477113 1|1:2.000:-5.00,-0.86,-0.07 1|1:2.000:-5.00,-1.05,-0.04 1|1:1.750:-1.34,-0.38,-0.27 1|1:1.900:-0.48,-0.48,-0.48 1|1:2.000:-0.48,-0.48,-0.48 1|1:1.650:-0.48,-0.48,-0.48 1|1:1.750:-4.70,-0.61,-0.12 1|1:2.000:-2.71,-0.46,-0.19 1|1:1.700:-0.48,-0.48,-0.48 1|1:1.750:-0.48,-0.48,-0.48 1|1:1.900:-1.71,-0.40,-0.24 1|1:1.950:-3.03,-0.46,-0.19 1|1:1.950:-2.49,-0.45,-0.19 1|1:2.000:-0.48,-0.48,-0.48 1|1:2.000:-0.48,-0.48,-0.48 diff --git a/test/vcf/record_test.cpp b/test/vcf/record_test.cpp index 32f170e45..73bf64372 100644 --- a/test/vcf/record_test.cpp +++ b/test/vcf/record_test.cpp @@ -156,7 +156,7 @@ namespace opencb { "0|1" }, std::make_shared(source)}) ); - CHECK_THROWS_AS( (vcf::Record{ + CHECK_NOTHROW( (vcf::Record{ "chr1", 123456, { "id123", "id456" }, @@ -167,8 +167,7 @@ namespace opencb { {"AN", "12"}, {"AF", "0.5"} }, { "GT", "DP" }, { "0|1" }, - std::make_shared(source)}), - std::invalid_argument); + std::make_shared(source)}) ); } SECTION("Same length alleles")