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GA4GHTT-232 - vcf4.4 initial changes #240

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Mar 20, 2024
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GA4GHTT-232 - vcf4.4 initial changes #240

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8 changes: 8 additions & 0 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -216,6 +216,7 @@ set (MOD_VCF_SOURCES
inc/vcf/validator_detail_v41.hpp
inc/vcf/validator_detail_v42.hpp
inc/vcf/validator_detail_v43.hpp
inc/vcf/validator_detail_v44.hpp
inc/vcf/validator.hpp

src/fasta/faidx.cpp
Expand Down Expand Up @@ -293,6 +294,7 @@ endif ()
set (V41_TESTS test/vcf/parser_v41_test.cpp)
set (V42_TESTS test/vcf/parser_v42_test.cpp)
set (V43_TESTS test/vcf/parser_v43_test.cpp)
set (V44_TESTS test/vcf/parser_v44_test.cpp)
set (ALL_TESTS
test/assembly_report/assembly_report_test.cpp
test/fasta/faidx_test.cpp
Expand All @@ -309,6 +311,7 @@ set (ALL_TESTS
test/vcf/parser_v41_test.cpp
test/vcf/parser_v42_test.cpp
test/vcf/parser_v43_test.cpp
test/vcf/parser_v44_test.cpp
test/vcf/predefined_info_tags_test.cpp
test/vcf/predefined_format_tags_test.cpp
test/vcf/record_cache_test.cpp
Expand All @@ -332,6 +335,11 @@ target_link_libraries (test_validator_v43 ${LIBRARIES_TO_LINK})
enable_testing ()
add_test (NAME ValidatorTests_v43 COMMAND test_validator_v43)

add_executable (test_validator_v44 test/main_test.cpp ${V44_TESTS})
target_link_libraries (test_validator_v44 ${LIBRARIES_TO_LINK})
enable_testing ()
add_test (NAME ValidatorTests_v44 COMMAND test_validator_v44)

add_executable (test_validation_suite test/main_test.cpp ${ALL_TESTS})
target_link_libraries (test_validation_suite ${LIBRARIES_TO_LINK})
enable_testing ()
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1 change: 1 addition & 0 deletions appveyor.yml
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Expand Up @@ -18,6 +18,7 @@ test_script:
- cmd: bin\test_validator_v41.exe
- cmd: bin\test_validator_v42.exe
- cmd: bin\test_validator_v43.exe
- cmd: bin\test_validator_v44.exe
- cmd: bin\test_validation_suite.exe

artifacts:
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4 changes: 4 additions & 0 deletions docs/developer-guide.md
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Expand Up @@ -41,6 +41,10 @@ executable binaries:

![architecture image](img/VCF-validator-architecture.png)

In case of dependent libraries being installed in non-standard paths,
update LIBRARY_PATH as shown below
'export LIBRARY_PATH=$LIBRARY_PATH:<path to required library's libpath>'

Comment on lines +44 to +47
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I'm not sure in which case this applies.
I've not seen this being used anywhere in the CMakeList.txt and it didn't alleviate my compilation issues.

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This could be useful when dependent libraries, expected to be available through OS, were installed in paths which are not part of library search. During Mac OS builds, I used to get link issues with zstd and icu libraries. They were present inside home-brew folders which were not part of any lib search environment variables.

Tried different ways to resolve them, like modifying CMake file, updating home-brew/cmake variables etc., and later noticed this from build.yml, as the easiest solution. Having this in dev-guide may help those building in Mac where many of the dependencies may be on a different path. (This seem to be applicable for linux builds as well but usually not required as installations usually made in standard search paths).

The role of Ragel and ODB in this project is explained further below.

## Code structure
Expand Down
75 changes: 74 additions & 1 deletion inc/vcf/file_structure.hpp
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Expand Up @@ -55,7 +55,8 @@ namespace ebi
{
v41,
v42,
v43
v43,
v44
};

enum class RecordType
Expand Down Expand Up @@ -159,6 +160,53 @@ namespace ebi
{ THOUSAND_G, { FLAG, "0" } }
};

const std::map<std::string, std::pair<std::string, std::string>> info_v44 = {
{ AA, { STRING, "1" } },
{ AC, { INTEGER, A } },
{ AD, { INTEGER, R } },
{ ADF, { INTEGER, R } },
{ ADR, { INTEGER, R } },
{ AF, { FLOAT, A } },
{ AN, { INTEGER, "1" } },
{ BKPTID, { STRING, UNKNOWN_CARDINALITY } },
{ BQ, { FLOAT, "1" } },
{ CICN, { INTEGER, "2" } },
{ CICNADJ, { INTEGER, UNKNOWN_CARDINALITY } },
{ CIEND, { INTEGER, "2" } },
{ CIGAR, { STRING, A } },
{ CILEN, { INTEGER, "2" } },
{ CIPOS, { INTEGER, "2" } },
{ CN, { INTEGER, "1" } },
{ CNADJ, { INTEGER, UNKNOWN_CARDINALITY } },
{ DB, { FLAG, "0" } },
{ DBRIPID, { STRING, "1" } },
{ DBVARID, { STRING, "1" } },
{ DGVID, { STRING, "1" } },
{ DP, { INTEGER, "1" } },
{ DPADJ, { INTEGER, UNKNOWN_CARDINALITY } },
{ END, { INTEGER, "1" } },
{ EVENT, { STRING, "1" } },
{ HOMLEN, { INTEGER, UNKNOWN_CARDINALITY } },
{ HOMSEQ, { STRING, UNKNOWN_CARDINALITY } },
{ H2, { FLAG, "0" } },
{ H3, { FLAG, "0" } },
{ IMPRECISE, { FLAG, "0" } },
{ MATEID, { STRING, UNKNOWN_CARDINALITY } },
{ MEINFO, { STRING, "4" } },
{ METRANS, { STRING, "4" } },
{ MQ, { MISSING_VALUE, "1" } },
{ MQ0, { INTEGER, "1" } },
{ NOVEL, { FLAG, "0" } },
{ NS, { INTEGER, "1" } },
{ PARID, { STRING, "1" } },
// TODO : SB metadata Type and Number is "."
{ SOMATIC, { FLAG, "0" } },
{ SVLEN, { INTEGER, UNKNOWN_CARDINALITY } },
{ SVTYPE, { STRING, "1" } },
{ VALIDATED, { FLAG, "0" } },
{ THOUSAND_G, { FLAG, "0" } }
};

const std::map<std::string, std::pair<std::string, std::string>> format_v41_v42 = {
{ AHAP, { INTEGER, "1" } },
{ CN, { INTEGER, "1" } },
Expand Down Expand Up @@ -206,6 +254,31 @@ namespace ebi
{ PS, { INTEGER, "1" } }
};

const std::map<std::string, std::pair<std::string, std::string>> format_v44 = {
{ AD, { INTEGER, R } },
{ ADF, { INTEGER, R } },
{ ADR, { INTEGER, R } },
{ AHAP, { INTEGER, "1" } },
{ CN, { INTEGER, "1" } },
{ CNL, { FLOAT, G } },
{ CNP, { FLOAT, G } },
{ CNQ, { FLOAT, "1" } },
{ DP, { INTEGER, "1" } },
{ EC, { INTEGER, A } },
{ FT, { STRING, "1" } },
{ GL, { FLOAT, G } },
{ GP, { FLOAT, G } },
{ GQ, { INTEGER, "1" } },
{ GT, { STRING, "1" } },
{ HAP, { INTEGER, "1" } },
{ HQ, { INTEGER, "2" } },
{ MQ, { INTEGER, "1" } },
{ NQ, { INTEGER, "1" } },
{ PL, { INTEGER, G } },
{ PQ, { INTEGER, "1" } },
{ PS, { INTEGER, "1" } }
};

const std::set<std::string> PREDEFINED_INFO_SVTYPES{
DEL,
INS,
Expand Down
1 change: 1 addition & 0 deletions inc/vcf/string_constants.hpp
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Expand Up @@ -27,6 +27,7 @@ namespace ebi
const std::string VCF_V41 = "VCFv4.1";
const std::string VCF_V42 = "VCFv4.2";
const std::string VCF_V43 = "VCFv4.3";
const std::string VCF_V44 = "VCFv4.4";

// validator, debugulator and assembly_checker command line arguments
const char STDIN[] = "stdin";
Expand Down
23 changes: 23 additions & 0 deletions inc/vcf/validator.hpp
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Expand Up @@ -172,6 +172,24 @@ namespace ebi
void parse_buffer(char const * p, char const * pe, char const * eof);
};

template <typename Configuration>
class ParserImpl_v44
: public ParserImpl,
Configuration::ParsePolicy,
Configuration::ErrorPolicy,
Configuration::OptionalPolicy
{
public:
using ParsePolicy = typename Configuration::ParsePolicy;
using ErrorPolicy = typename Configuration::ErrorPolicy;
using OptionalPolicy = typename Configuration::OptionalPolicy;

ParserImpl_v44(std::shared_ptr<Source> source, AdditionalChecks additionalChecks);

private:
void parse_buffer(char const * p, char const * pe, char const * eof);
};

// Predefined aliases for common uses of the parser
using QuickValidator_v41 = ParserImpl_v41<QuickValidatorCfg>;
using FullValidator_v41 = ParserImpl_v41<FullValidatorCfg>;
Expand All @@ -185,6 +203,10 @@ namespace ebi
using FullValidator_v43 = ParserImpl_v43<FullValidatorCfg>;
using Reader_v43 = ParserImpl_v43<ReaderCfg>;

using QuickValidator_v44 = ParserImpl_v44<QuickValidatorCfg>;
using FullValidator_v44 = ParserImpl_v44<FullValidatorCfg>;
using Reader_v44 = ParserImpl_v44<ReaderCfg>;

bool is_valid_vcf_file(std::istream &input, const std::string &sourceName,
ValidationLevel validationLevel,
std::vector<std::unique_ptr<ebi::vcf::ReportWriter>> &outputs,
Expand All @@ -210,5 +232,6 @@ namespace ebi
#include "validator_detail_v41.hpp"
#include "validator_detail_v42.hpp"
#include "validator_detail_v43.hpp"
#include "validator_detail_v44.hpp"

#endif // VCF_VALIDATOR_HPP
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