, including all inherited members.
| addFilterFlag(std::ostream &out, const std::string &flag, bool &filtered) const | cgatools::junctions::JunctionVcfWriter | |
| convertMobileElementToVcf(const std::string &med) const | cgatools::junctions::JunctionVcfWriter | |
| createJunctionVcfId(const JunctionRef &jref, size_t side) const | cgatools::junctions::JunctionVcfWriter | |
| fileFieldSeparator_ (defined in cgatools::junctions::JunctionVcfWriter) | cgatools::junctions::JunctionVcfWriter | |
| filterScoreThreshold_ (defined in cgatools::junctions::JunctionVcfWriter) | cgatools::junctions::JunctionVcfWriter | |
| filterSideLength_ (defined in cgatools::junctions::JunctionVcfWriter) | cgatools::junctions::JunctionVcfWriter | |
| formatPositionForVcf(reference::Location pos, const std::string &sep) const | cgatools::junctions::JunctionVcfWriter | |
| init() | cgatools::junctions::JunctionVcfWriter | [protected] |
| junctionFiles_ (defined in cgatools::junctions::JunctionVcfWriter) | cgatools::junctions::JunctionVcfWriter | [protected] |
| JunctionVcfWriter(boost::shared_ptr< reference::CrrFile > ref, boost::shared_ptr< junctions::JunctionFiles > junctionFiles) (defined in cgatools::junctions::JunctionVcfWriter) | cgatools::junctions::JunctionVcfWriter | |
| JunctionVcfWriter() (defined in cgatools::junctions::JunctionVcfWriter) | cgatools::junctions::JunctionVcfWriter | [protected] |
| reference_ (defined in cgatools::junctions::JunctionVcfWriter) | cgatools::junctions::JunctionVcfWriter | [protected] |
| sampleIds_ (defined in cgatools::junctions::JunctionVcfWriter) | cgatools::junctions::JunctionVcfWriter | [protected] |
| writeJunctionAltFieldToVcf(const JunctionRef &jref, size_t side, std::ostream &out, bool suppressChrom=false) const | cgatools::junctions::JunctionVcfWriter | |
| writeJunctionComparisonField(const JunctionRef &jref, size_t side, std::ostream &out) const | cgatools::junctions::JunctionVcfWriter | |
| writeJunctionFilterFieldToVcf(const JunctionRef &jref, std::ostream &out) const | cgatools::junctions::JunctionVcfWriter | |
| writeJunctionInfoFieldToVcf(const JunctionRef &jref, size_t side, std::ostream &out) const | cgatools::junctions::JunctionVcfWriter | |
| writeJunctionPositionToVcf(const junctions::JunctionSideSection &jss, size_t side, std::ostream &out) const (defined in cgatools::junctions::JunctionVcfWriter) | cgatools::junctions::JunctionVcfWriter | |
| writeJunctionToVcf(const JunctionRef &jref, size_t side, const JunctionCompatMapPerFile &compat, std::ostream &out) const | cgatools::junctions::JunctionVcfWriter | |
| writeJunctionVcfHeaders(std::ostream &out) const | cgatools::junctions::JunctionVcfWriter | |
1.6.2
