Classes | |
| struct | HaploEntry |
| struct | VcfData |
Public Member Functions | |
| VariantFileVcfRecordWriter (const std::vector< boost::shared_ptr< VariantFileIterator > > &var, const std::vector< std::string > &fieldNames, const cgatools::reference::CrrFile &crr, const std::string &calibPrefix) | |
| cgatools::reference::Location | getLocation () const |
| Get 0-based location of first base of VCF record. | |
| void | writeRef (std::ostream &out) const |
| Write REF field of VCF record. | |
| void | writeAlt (std::ostream &out) const |
| Write ALT field of VCF record. | |
| void | writeInfo (std::ostream &out) const |
| Write INFO field of VCF record. | |
| void | writeFormat (std::ostream &out) const |
| Write FORMAT field of VCF record. | |
| void | writeSample (std::ostream &out, size_t gIdx) const |
| Write per-sample field of VCF record, for the given genome. | |
| const VcfData & | getRecord () const |
|
const cgatools::reference::CrrFile & | getCrr () const |
| void | setLocus (const cgatools::reference::Range &range, const Superlocus &sl, std::vector< PhasedHypothesis > &hyp) |
| size_t | getSampleCount () const |
| const char * | getSomaticStatusAnnotation (size_t gIdx, const std::vector< std::vector< SubFieldCall > > &calls) const |
| void | addSubFieldHeaderRecords (std::vector< cgatools::conv::VcfSubFieldHeaderRecord > &result) const |
| size_t | getAlleleCount (size_t alleleIdx) const |
| cgatools::reference::Location cgatools::variants::VariantFileVcfRecordWriter::getLocation | ( | ) | const [virtual] |
Get 0-based location of first base of VCF record.
The value output to the VCF file is at Location.offset+1.
Implements cgatools::conv::VcfRecordWriter.
| void cgatools::variants::VariantFileVcfRecordWriter::writeSample | ( | std::ostream & | out, | |
| size_t | idxGenome | |||
| ) | const [virtual] |
Write per-sample field of VCF record, for the given genome.
Genomes are numbered starting with 0 for the first genome.
Implements cgatools::conv::VcfRecordWriter.
1.6.2
