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| FlowCaller (const PathPositionHandleGraph &graph, SupportBasedSnarlCaller &snarl_caller, SnarlManager &snarl_manager, const string &sample_name, TraversalFinder &traversal_finder, const vector< string > &ref_paths={}, const vector< size_t > &ref_path_offsets={}, ostream &out_stream=cout) |
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virtual | ~FlowCaller () |
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virtual bool | call_snarl (const Snarl &snarl, int ploidy) |
| Call a given snarl, and print the output to out_stream. More...
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virtual string | vcf_header (const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides={}) const |
| Write the vcf header (version and contigs and basic info) More...
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| GraphCaller (SnarlCaller &snarl_caller, SnarlManager &snarl_manager, ostream &out_stream=cout) |
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virtual | ~GraphCaller () |
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virtual void | call_top_level_snarls (int ploidy, bool recurse_on_fail=true) |
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| VCFOutputCaller (const string &sample_name) |
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virtual | ~VCFOutputCaller () |
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void | add_variant (vcflib::Variant &var) const |
| Add a variant to our buffer. More...
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void | write_variants (ostream &out_stream) const |
| Sort then write variants in the buffer. More...
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void | emit_variant (const PathPositionHandleGraph &graph, SnarlCaller &snarl_caller, const Snarl &snarl, const vector< SnarlTraversal > &called_traversals, const vector< int > &genotype, int ref_trav_idx, const unique_ptr< SnarlCaller::CallInfo > &call_info, const string &ref_path_name, int ref_offset) const |
| print a vcf variant More...
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tuple< size_t, size_t, bool, step_handle_t, step_handle_t > | get_ref_interval (const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) const |
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void | flatten_common_allele_ends (vcflib::Variant &variant, bool backward) const |
| clean up the alleles to not share common prefixes / suffixes More...
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FlowCaller : Uses any traversals finder (ex, FlowTraversalFinder) to find traversals, and calls those based on how much support they have.
Should work on any graph but will not report cyclic traversals. Does not (yet, anyway) support nested calling, so the entire site is processes in one shot. Designed to replace LegacyCaller, as it should miss fewer obviously good traversals, and is not dependent on old protobuf-based structures.