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

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

add_variant(vcflib::Variant &var) constvg::VCFOutputCaller
break_chain(const HandleGraph &graph, const Chain &chain, size_t max_edges, size_t max_trivial)vg::GraphCallerprotected
call_snarl(const Snarl &snarl, int ploidy)vg::VCFGenotypervirtual
call_top_level_chains(const HandleGraph &graph, int ploidy, size_t max_edges, size_t max_trivial, bool recurse_on_fail=true)vg::GraphCallervirtual
call_top_level_snarls(const HandleGraph &graph, int ploidy, bool recurse_on_fail=true)vg::GraphCallervirtual
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) constvg::VCFOutputCallerprotected
emittervg::GAFOutputCallerprotected
flatten_common_allele_ends(vcflib::Variant &variant, bool backward, size_t len_override) constvg::VCFOutputCallerprotected
gaf_outputvg::VCFGenotyperprotected
gaf_sample_namevg::GAFOutputCallerprotected
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) constvg::VCFOutputCallerprotected
get_ref_positions(const vector< vcflib::Variant * > &variants) constvg::VCFGenotyperprotected
graphvg::VCFGenotyperprotected
GraphCaller(SnarlCaller &snarl_caller, SnarlManager &snarl_manager)vg::GraphCaller
input_vcfvg::VCFGenotyperprotected
max_uncalled_allelesvg::VCFOutputCallerprotected
output_variantsvg::VCFOutputCallermutableprotected
output_vcfvg::VCFOutputCallermutableprotected
pad_traversal(const PathHandleGraph &graph, const SnarlTraversal &trav) constvg::GAFOutputCaller
ref_pathsvg::GAFOutputCallerprotected
sample_namevg::VCFOutputCallerprotected
scan_contig_lengths() constvg::VCFGenotyperprotectedvirtual
snarl_callervg::GraphCallerprotected
snarl_managervg::GraphCallerprotected
trav_paddingvg::GAFOutputCallerprotected
traversal_findervg::VCFGenotyperprotected
traversals_onlyvg::VCFGenotyperprotected
vcf_header(const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides={}) constvg::VCFGenotypervirtual
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) constvg::VCFOutputCaller
~GAFOutputCaller()vg::GAFOutputCallervirtual
~GraphCaller()vg::GraphCallervirtual
~VCFGenotyper()vg::VCFGenotypervirtual
~VCFOutputCaller()vg::VCFOutputCallervirtual