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| LegacyCaller (const PathPositionHandleGraph &graph, SupportBasedSnarlCaller &snarl_caller, SnarlManager &snarl_manager, const string &sample_name, const vector< string > &ref_paths={}, const vector< size_t > &ref_path_offsets={}) |
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virtual | ~LegacyCaller () |
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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) |
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virtual | ~GraphCaller () |
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virtual void | call_top_level_snarls (const HandleGraph &graph, int ploidy, bool recurse_on_fail=true) |
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virtual void | call_top_level_chains (const HandleGraph &graph, int ploidy, size_t max_edges, size_t max_trivial, 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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pair< vector< SnarlTraversal >, vector< int > > | top_down_genotype (const Snarl &snarl, TraversalFinder &trav_finder, int ploidy, const string &ref_path_name, pair< size_t, size_t > ref_interval) const |
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SnarlTraversal | get_reference_traversal (const Snarl &snarl, TraversalFinder &trav_finder) const |
| we need the reference traversal for VCF, but if the ref is not called, the above method won't find it. More...
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tuple< vector< SnarlTraversal >, vector< int >, unique_ptr< SnarlCaller::CallInfo > > | re_genotype (const Snarl &snarl, TraversalFinder &trav_finder, const vector< SnarlTraversal > &in_traversals, const vector< int > &in_genotype, int ploidy, const string &ref_path_name, pair< size_t, size_t > ref_interval) const |
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bool | is_traversable (const Snarl &snarl) |
| check if a site can be handled by the RepresentativeTraversalFinder More...
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pair< string, PathIndex * > | find_index (const Snarl &snarl, const vector< PathIndex * > path_indexes) const |
| look up a path index for a site and return its name too More...
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vector< Chain > | break_chain (const HandleGraph &graph, const Chain &chain, size_t max_edges, size_t max_trivial) |
| Break up a chain into bits that we want to call using size heuristics. 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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LegacyCaller : Preserves (most of) the old vg call logic by using the RepresentativeTraversalFinder to recursively find traversals through arbitrary sites.