vg
tools for working with variation graphs
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This is the complete list of members for vg::MCMCCaller, including all inherited members.
add_variant(vcflib::Variant &var) const | vg::VCFOutputCaller | |
call_snarl(const Snarl &snarl) | vg::MCMCCaller | protected |
call_top_level_snarls(bool recurse_on_fail=true) | vg::MCMCCaller | |
emit_variant(const Snarl &snarl, const vector< int > &genotype, SnarlTraversal ref_trav, const string &ref_path_name, const vector< SnarlTraversal > &haplo_travs) const | vg::MCMCCaller | protected |
vg::VCFOutputCaller::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 |
flatten_common_allele_ends(vcflib::Variant &variant, bool backward) const | vg::MCMCCaller | protected |
vg::VCFOutputCaller::flatten_common_allele_ends(vcflib::Variant &variant, bool backward, size_t len_override) const | vg::VCFOutputCaller | protected |
genome | vg::MCMCCaller | |
get_ref_interval(const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) const | vg::VCFOutputCaller | protected |
get_ref_position(const Snarl &snarl, const string &ref_path_name) const | vg::MCMCCaller | protected |
is_traversable(const Snarl &snarl) | vg::MCMCCaller | protected |
max_uncalled_alleles | vg::VCFOutputCaller | protected |
MCMCCaller(const PathPositionHandleGraph *path_position_handle_graph, PhasedGenome &genome, SnarlManager &snarl_manager, const string &sample_name, const vector< string > &ref_paths={}, const vector< size_t > &ref_path_offsets={}, const vector< size_t > &ref_path_lengths={}, ostream &out_stream=cout) | vg::MCMCCaller | |
out_stream | vg::MCMCCaller | |
output_variants | vg::VCFOutputCaller | mutableprotected |
output_vcf | vg::VCFOutputCaller | mutableprotected |
path_position_handle_graph | vg::MCMCCaller | protected |
ref_offsets | vg::MCMCCaller | protected |
ref_path_lengths | vg::MCMCCaller | |
ref_path_offsets | vg::MCMCCaller | |
ref_paths | vg::MCMCCaller | protected |
sample_name | vg::MCMCCaller | |
snarl_manager | vg::MCMCCaller | |
trav | vg::MCMCCaller | |
update_vcf_info(const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype, const string &sample_name, vcflib::Variant &variant) const | vg::MCMCCaller | protected |
vcf_header(const PathPositionHandleGraph &graph, const vector< string > &ref_paths, const vector< size_t > &contig_length_overrides) const | vg::MCMCCaller | virtual |
vg::VCFOutputCaller::vcf_header(const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides) const | vg::VCFOutputCaller | virtual |
VCFOutputCaller(const string &sample_name) | vg::VCFOutputCaller | |
write_variants(ostream &out_stream) const | vg::VCFOutputCaller | |
~MCMCCaller() | vg::MCMCCaller | virtual |
~VCFOutputCaller() | vg::VCFOutputCaller | virtual |