|
| 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, AlignmentEmitter *aln_emitter, bool traversals_only, bool gaf_output, size_t trav_padding, bool genotype_snarls) |
|
virtual | ~FlowCaller () |
|
virtual bool | call_snarl (const Snarl &snarl, int ploidy) |
| Call a given snarl, and print the output to out_stream. More...
|
|
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...
|
|
| GraphCaller (SnarlCaller &snarl_caller, SnarlManager &snarl_manager) |
|
virtual | ~GraphCaller () |
|
virtual void | call_top_level_snarls (const HandleGraph &graph, int ploidy, bool recurse_on_fail=true) |
|
virtual void | call_top_level_chains (const HandleGraph &graph, int ploidy, size_t max_edges, size_t max_trivial, bool recurse_on_fail=true) |
|
| VCFOutputCaller (const string &sample_name) |
|
virtual | ~VCFOutputCaller () |
|
void | add_variant (vcflib::Variant &var) const |
| Add a variant to our buffer. More...
|
|
void | write_variants (ostream &out_stream) const |
| Sort then write variants in the buffer. More...
|
|
| 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...
|
|
virtual | ~GAFOutputCaller () |
|
void | emit_gaf_traversals (const PathHandleGraph &graph, const vector< SnarlTraversal > &travs) |
| print the GAF traversals More...
|
|
void | emit_gaf_variant (const HandleGraph &graph, const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype) |
| print the GAF genotype More...
|
|
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...
|
|
|
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...
|
|
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...
|
|
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 |
|
void | flatten_common_allele_ends (vcflib::Variant &variant, bool backward, size_t len_override) const |
|
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.