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| VCFGenotyper (const PathHandleGraph &graph, SnarlCaller &snarl_caller, SnarlManager &snarl_manager, vcflib::VariantCallFile &variant_file, const string &sample_name, const vector< string > &ref_paths, FastaReference *ref_fasta, FastaReference *ins_fasta, AlignmentEmitter *aln_emitter, bool traversals_only, bool gaf_output, size_t trav_padding) |
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virtual | ~VCFGenotyper () |
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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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| GAFOutputCaller (AlignmentEmitter *emitter, const string &sample_name, const vector< string > &ref_paths, size_t trav_padding) |
| The emitter object is created and owned by external forces. More...
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virtual | ~GAFOutputCaller () |
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void | emit_gaf_traversals (const PathHandleGraph &graph, const vector< SnarlTraversal > &travs) |
| print the GAF traversals More...
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void | emit_gaf_variant (const HandleGraph &graph, const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype) |
| print the GAF genotype More...
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SnarlTraversal | pad_traversal (const PathHandleGraph &graph, const SnarlTraversal &trav) const |
| pad a traversal with (first found) reference path, adding up to trav_padding to each side More...
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tuple< string, size_t, size_t > | get_ref_positions (const vector< vcflib::Variant * > &variants) const |
| get path positions bounding a set of variants More...
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virtual unordered_map< string, size_t > | scan_contig_lengths () const |
| munge out the contig lengths from the VCF header 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, bool genotype_snarls) 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, size_t len_override) const |
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VCFGenotyper : Genotype variants in a given VCF file