Classes | |
| class | CallFilter |
| struct | LocusData |
| Locus data in OLPL file. | |
Public Member Functions | |
| VariantFileIterator (const CrrFile &crr) | |
| void | open (const std::string &fn) |
| void | close () |
| bool | eof () const |
| const Locus & | operator* () const |
| const Locus * | operator-> () const |
| VariantFileIterator & | operator++ () |
| const std::string & | getFileName () |
| void | error (const std::string &msg) const |
| void | locusCallError (const std::string &msg, const Locus &locus, const Call &call) const |
| void | locusError (const std::string &msg, const Locus &locus) const |
| void | setReferenceCoverValidation (bool validate) |
|
const util::DelimitedFile::Metadata & | getMetadata () const |
| const std::vector< std::string > & | getColumnHeaders () const |
| const std::vector< std::string > & | getAnnotationColumnHeaders () const |
| bool | xRefIsAlleleSpecific () const |
| const std::string & | getFilterString () const |
| void | getReadCounts (int32_t *allele1ReadCount, int32_t *allele2ReadCount, int32_t *referenceAlleleReadCount, int32_t *totalReadCount, cgdata::EvidenceReader &evidence, const Locus &locus) const |
| Returns the requested read counts, as defined in the masterVar file, or -1 if this read count is empty as annotated in a masterVar file. | |
| bool | hasAnnotation (const std::string &name) const |
| size_t | getAnnotationIndex (const std::string &name) const |
| Returns the index of a given annotation column in the Locus::extras_ vector, or Locus::extras_.size() if the annotation is not present. | |
| void | fillOlplFileMetadata (util::DelimitedFile::Metadata &meta) const |
| void | writeOlplFileHeader (std::ostream &out) const |
| bool | isOlpl () const |
| size_t cgatools::variants::VariantFileIterator::getAnnotationIndex | ( | const std::string & | name | ) | const |
Returns the index of a given annotation column in the Locus::extras_ vector, or Locus::extras_.size() if the annotation is not present.
| void cgatools::variants::VariantFileIterator::getReadCounts | ( | int32_t * | allele1ReadCount, | |
| int32_t * | allele2ReadCount, | |||
| int32_t * | referenceAlleleReadCount, | |||
| int32_t * | totalReadCount, | |||
| cgdata::EvidenceReader & | evidence, | |||
| const Locus & | locus | |||
| ) | const |
Returns the requested read counts, as defined in the masterVar file, or -1 if this read count is empty as annotated in a masterVar file.
If the input file does not have read count annotations, the read counts are computed from the evidence.
1.6.2
