vg
tools for working with variation graphs
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This is the complete list of members for vg::VCFGenotyper, including all inherited members.
add_variant(vcflib::Variant &var) const | vg::VCFOutputCaller | |
break_chain(const HandleGraph &graph, const Chain &chain, size_t max_edges, size_t max_trivial) | vg::GraphCaller | protected |
call_snarl(const Snarl &snarl, int ploidy) | vg::VCFGenotyper | virtual |
call_top_level_chains(const HandleGraph &graph, int ploidy, size_t max_edges, size_t max_trivial, bool recurse_on_fail=true) | vg::GraphCaller | virtual |
call_top_level_snarls(const HandleGraph &graph, int ploidy, bool recurse_on_fail=true) | vg::GraphCaller | virtual |
emit_gaf_traversals(const PathHandleGraph &graph, const vector< SnarlTraversal > &travs) | vg::GAFOutputCaller | |
emit_gaf_variant(const HandleGraph &graph, const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype) | vg::GAFOutputCaller | |
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 | vg::VCFOutputCaller | protected |
emitter | vg::GAFOutputCaller | protected |
flatten_common_allele_ends(vcflib::Variant &variant, bool backward, size_t len_override) const | vg::VCFOutputCaller | protected |
gaf_output | vg::VCFGenotyper | protected |
gaf_sample_name | vg::GAFOutputCaller | protected |
GAFOutputCaller(AlignmentEmitter *emitter, const string &sample_name, const vector< string > &ref_paths, size_t trav_padding) | vg::GAFOutputCaller | |
get_ref_interval(const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) const | vg::VCFOutputCaller | protected |
get_ref_positions(const vector< vcflib::Variant * > &variants) const | vg::VCFGenotyper | protected |
graph | vg::VCFGenotyper | protected |
GraphCaller(SnarlCaller &snarl_caller, SnarlManager &snarl_manager) | vg::GraphCaller | |
input_vcf | vg::VCFGenotyper | protected |
max_uncalled_alleles | vg::VCFOutputCaller | protected |
output_variants | vg::VCFOutputCaller | mutableprotected |
output_vcf | vg::VCFOutputCaller | mutableprotected |
pad_traversal(const PathHandleGraph &graph, const SnarlTraversal &trav) const | vg::GAFOutputCaller | |
ref_paths | vg::GAFOutputCaller | protected |
sample_name | vg::VCFOutputCaller | protected |
scan_contig_lengths() const | vg::VCFGenotyper | protectedvirtual |
snarl_caller | vg::GraphCaller | protected |
snarl_manager | vg::GraphCaller | protected |
trav_padding | vg::GAFOutputCaller | protected |
traversal_finder | vg::VCFGenotyper | protected |
traversals_only | vg::VCFGenotyper | protected |
vcf_header(const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides={}) const | vg::VCFGenotyper | virtual |
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) | vg::VCFGenotyper | |
VCFOutputCaller(const string &sample_name) | vg::VCFOutputCaller | |
write_variants(ostream &out_stream) const | vg::VCFOutputCaller | |
~GAFOutputCaller() | vg::GAFOutputCaller | virtual |
~GraphCaller() | vg::GraphCaller | virtual |
~VCFGenotyper() | vg::VCFGenotyper | virtual |
~VCFOutputCaller() | vg::VCFOutputCaller | virtual |