, including all inherited members.
| add(std::vector< cgatools::conv::VcfSubFieldHeaderRecord > &result, cgatools::conv::VcfSubFieldHeaderRecord::Key key, const std::string &id, const std::string &number, const std::string &type, const std::string &description) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| addFilterFlag(const std::string &flag, bool &filtered) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| copyJunctionListForVcf(const junctions::JunctionRefs &jrl, std::vector< JunctionRefSide > &out, JunctionCompatMapPerFile &compat) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| createRecord(const JunctionRef &jref, size_t side, const JunctionCompatMapPerFile &compat) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| crr_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| currentRecord_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| distanceTolerance_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| eof() const | cgatools::junctions::JunctionVcfRecordSource | [virtual] |
| fieldNames_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| fieldNameSet_ (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| getAltField(const JunctionRef &jref, size_t side, bool suppressChrom=false) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| getAssemblyId(size_t idxGenome) const | cgatools::junctions::JunctionVcfRecordSource | [virtual] |
| getFormat(const JunctionRef &jref, size_t side) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| getId(const JunctionRef &jref, size_t side) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| getInfo(const JunctionRef &jref, size_t side) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| getKeyValueHeaderRecords(size_t idxGenome) const | cgatools::junctions::JunctionVcfRecordSource | [virtual] |
| getMEI(const std::string &med) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| getPosition(reference::Location pos, const std::string &sep) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| getSample(const JunctionRef &jref, size_t side, size_t idx, const JunctionCompatMapPerFile &compat) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| getSample(const JunctionRef &jref, size_t side) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| getSampleFilter(const JunctionRef &jref) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| getSource(size_t idxGenome) const | cgatools::junctions::JunctionVcfRecordSource | [virtual] |
| getSubFieldHeaderRecords() const | cgatools::junctions::JunctionVcfRecordSource | [virtual] |
| junctionFileNames_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| junctionFiles_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| junctionLengthThreshold_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| JunctionVcfRecordSource(const std::vector< boost::shared_ptr< cgatools::cgdata::GenomeMetadata > > &genomes, const std::vector< std::string > &junctionFileNames, const std::vector< std::string > fieldNames, const cgatools::reference::CrrFile &crr, size_t scoreThreshold=10, size_t sideLengthThreshold_=70, size_t distanceTolerance=200, size_t junctionLengthThreshold=500, bool normalPriorityOutput=false, bool useHighConfidenceJunctionsForTumor=true) (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | |
| need(const std::string &fieldName) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| normalPriorityOutput_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| operator*() const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [virtual] |
| operator++() (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [virtual] |
| operator->() const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [virtual] |
| pickDefaultMatch(const JunctionRef &jr, JunctionRefSet &junctionsToSuppress) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| pickNormalPriorityMatch(const JunctionRef &jr, JunctionRefSet &junctionsToSuppress) const (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| records_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| run() (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | |
| run1Genome() (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| run2Genomes() (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| sampleFieldIDs_ (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected, static] |
| sampleIds_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| scoreThreshold_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| sideLengthThreshold_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| useHighConfidenceJunctionsForTumor_ (defined in cgatools::junctions::JunctionVcfRecordSource) | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| writeAllFields(bool v) | cgatools::junctions::JunctionVcfRecordSource | |
| writeAllFields_ | cgatools::junctions::JunctionVcfRecordSource | [protected] |
| ~VcfRecordSource() (defined in cgatools::conv::VcfRecordSource) | cgatools::conv::VcfRecordSource | [inline, virtual] |
1.6.2
