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

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

add_allele_path_to_info(const HandleGraph *graph, vcflib::Variant &v, int allele, const Traversal &trav, bool reversed, bool one_based) constvg::VCFOutputCallerprotected
add_allele_path_to_info(vcflib::Variant &v, int allele, const SnarlTraversal &trav, bool reversed, bool one_based) constvg::VCFOutputCallerprotected
add_variant(vcflib::Variant &var) constvg::VCFOutputCaller
alignment_emittervg::NestedFlowCallerprotected
break_chain(const HandleGraph &graph, const Chain &chain, size_t max_edges, size_t max_trivial)vg::GraphCallerprotected
call_snarl(const Snarl &snarl)vg::NestedFlowCallervirtual
call_snarl_recursive(const Snarl &managed_snarl, int ploidy, const string &parent_ref_path_name, pair< size_t, size_t > parent_ref_path_interval, CallTable &call_table)vg::NestedFlowCallerprotected
call_top_level_chains(const HandleGraph &graph, size_t max_edges, size_t max_trivial, RecurseType recurise_type=RecurseOnFail)vg::GraphCallervirtual
call_top_level_snarls(const HandleGraph &graph, RecurseType recurse_type=RecurseOnFail)vg::GraphCallervirtual
CallTable typedefvg::NestedFlowCallerprotected
emit_gaf_traversals(const PathHandleGraph &graph, const string &snarl_name, const vector< SnarlTraversal > &travs, int64_t ref_trav_idx, const string &ref_path_name, int64_t ref_path_position, const TraversalSupportFinder *support_finder=nullptr)vg::GAFOutputCaller
emit_gaf_variant(const PathHandleGraph &graph, const string &snarl_name, const vector< SnarlTraversal > &travs, const vector< int > &genotype, int64_t ref_trav_idx, const string &ref_path_name, int64_t ref_path_position, const TraversalSupportFinder *support_finder=nullptr)vg::GAFOutputCaller
emit_snarl_recursive(const Snarl &managed_snarl, int ploidy, CallTable &call_table)vg::NestedFlowCallerprotected
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, int ploidy, function< string(const vector< SnarlTraversal > &, const vector< int > &, int, int, int)> trav_to_string=nullptr)vg::VCFOutputCallerprotected
emittervg::GAFOutputCallerprotected
flatten_alt_allele(const string &nested_allele, int allele, int ploidy, const CallTable &call_table) constvg::NestedFlowCallerprotected
flatten_common_allele_ends(vcflib::Variant &variant, bool backward, size_t len_override) constvg::VCFOutputCallerprotected
flatten_reference_allele(const string &nested_allele, const CallTable &call_table) constvg::NestedFlowCallerprotected
gaf_outputvg::NestedFlowCallerprotected
gaf_sample_namevg::GAFOutputCallerprotected
GAFOutputCaller(AlignmentEmitter *emitter, const string &sample_name, const vector< string > &ref_paths, size_t trav_padding)vg::GAFOutputCaller
genotype_snarlsvg::NestedFlowCallerprotected
get_ref_interval(const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) constvg::VCFOutputCallerprotected
get_ref_position(const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name, int64_t ref_path_offset) constvg::VCFOutputCallerprotected
graphvg::NestedFlowCallerprotected
GraphCaller(SnarlCaller &snarl_caller, SnarlManager &snarl_manager)vg::GraphCaller
include_nestedvg::VCFOutputCallerprotected
max_snarl_shallow_sizevg::NestedFlowCallerprotected
max_uncalled_allelesvg::VCFOutputCallerprotected
max_vcf_line_lengthvg::VCFOutputCallerprotectedstatic
nested_support_findervg::NestedFlowCallerprotected
NestedFlowCaller(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, const vector< int > &ref_path_ploidies, AlignmentEmitter *aln_emitter, bool traversals_only, bool gaf_output, size_t trav_padding, bool genotype_snarls)vg::NestedFlowCaller
output_variantsvg::VCFOutputCallermutableprotected
output_vcfvg::VCFOutputCallermutableprotected
pad_traversal(const PathHandleGraph &graph, const SnarlTraversal &trav) constvg::GAFOutputCaller
print_snarl(const HandleGraph *grpah, const handle_t &snarl_start, const handle_t &snarl_end, bool in_brackets=false) constvg::VCFOutputCallerprotected
print_snarl(const Snarl &snarl, bool in_brackets=false) constvg::VCFOutputCallerprotected
RecurseAlways enum valuevg::GraphCaller
RecurseNever enum valuevg::GraphCaller
RecurseOnFail enum valuevg::GraphCaller
RecurseType enum namevg::GraphCaller
ref_offsetsvg::NestedFlowCallerprotected
ref_path_setvg::NestedFlowCallerprotected
ref_pathsvg::NestedFlowCallerprotected
ref_ploidiesvg::NestedFlowCallerprotected
sample_namevg::VCFOutputCallerprotected
scan_snarl(const string &allele_string, function< void(const string &, Snarl &)> callback) constvg::VCFOutputCallerprotected
set_nested(bool nested)vg::VCFOutputCaller
set_show_progress(bool show_progress)vg::GraphCaller
set_translation(const unordered_map< nid_t, pair< string, size_t >> *translation)vg::VCFOutputCaller
show_progressvg::GraphCallerprotected
snarl_callervg::GraphCallerprotected
snarl_managervg::GraphCallerprotected
translationvg::VCFOutputCallerprotected
trav_paddingvg::GAFOutputCallerprotected
trav_string(const HandleGraph &graph, const SnarlTraversal &trav) constvg::VCFOutputCallerprotected
traversal_findervg::NestedFlowCallerprotected
traversals_onlyvg::NestedFlowCallerprotected
update_nesting_info_tags(const SnarlManager *snarl_manager)vg::VCFOutputCallerprotected
vcf_fixup(vcflib::Variant &var) constvg::VCFOutputCaller
vcf_header(const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides={}) constvg::NestedFlowCallervirtual
VCFOutputCaller(const string &sample_name)vg::VCFOutputCaller
write_variants(ostream &out_stream, const SnarlManager *snarl_manager=nullptr)vg::VCFOutputCaller
~GAFOutputCaller()vg::GAFOutputCallervirtual
~GraphCaller()vg::GraphCallervirtual
~NestedFlowCaller()vg::NestedFlowCallervirtual
~VCFOutputCaller()vg::VCFOutputCallervirtual