vg
tools for working with variation graphs
vg::MCMCCaller Member List

This is the complete list of members for vg::MCMCCaller, including all inherited members.

add_variant(vcflib::Variant &var) constvg::VCFOutputCaller
call_snarl(const Snarl &snarl)vg::MCMCCallerprotected
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) constvg::MCMCCallerprotected
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) constvg::VCFOutputCallerprotected
flatten_common_allele_ends(vcflib::Variant &variant, bool backward) constvg::MCMCCallerprotected
vg::VCFOutputCaller::flatten_common_allele_ends(vcflib::Variant &variant, bool backward, size_t len_override) constvg::VCFOutputCallerprotected
genomevg::MCMCCaller
get_ref_interval(const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) constvg::VCFOutputCallerprotected
get_ref_position(const Snarl &snarl, const string &ref_path_name) constvg::MCMCCallerprotected
is_traversable(const Snarl &snarl)vg::MCMCCallerprotected
max_uncalled_allelesvg::VCFOutputCallerprotected
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_streamvg::MCMCCaller
output_variantsvg::VCFOutputCallermutableprotected
output_vcfvg::VCFOutputCallermutableprotected
path_position_handle_graphvg::MCMCCallerprotected
ref_offsetsvg::MCMCCallerprotected
ref_path_lengthsvg::MCMCCaller
ref_path_offsetsvg::MCMCCaller
ref_pathsvg::MCMCCallerprotected
sample_namevg::MCMCCaller
snarl_managervg::MCMCCaller
travvg::MCMCCaller
update_vcf_info(const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype, const string &sample_name, vcflib::Variant &variant) constvg::MCMCCallerprotected
vcf_header(const PathPositionHandleGraph &graph, const vector< string > &ref_paths, const vector< size_t > &contig_length_overrides) constvg::MCMCCallervirtual
vg::VCFOutputCaller::vcf_header(const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides) constvg::VCFOutputCallervirtual
VCFOutputCaller(const string &sample_name)vg::VCFOutputCaller
write_variants(ostream &out_stream) constvg::VCFOutputCaller
~MCMCCaller()vg::MCMCCallervirtual
~VCFOutputCaller()vg::VCFOutputCallervirtual