Public Member Functions | |
| CnvFileVcfRecordWriter (const std::vector< std::string > cnvFieldNames, const cgatools::reference::CrrFile &crr, int numGenomes, bool someSomatic, bool someNonsomaticLAF) | |
| 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. | |
| void | setDiploidData (diploidData &data, int gIdx) |
| void | setNondiploidData (nondiploidData &data, int gIdx) |
| void | setSomaticData (somaticData &data, int gIdx) |
| cgatools::reference::Range | getDiploidRange (int gIdx) const |
| cgatools::reference::Range | getNondiploidRange (int gIdx) const |
| cgatools::reference::Range | getSomaticRange (int gIdx) const |
| bool | isDeferred (int gIdx) const |
| void | setDeferred (int gIdx, bool status) |
| cgatools::reference::Location cgatools::copynumber::CnvFileVcfRecordWriter::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::copynumber::CnvFileVcfRecordWriter::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
