vg
tools for working with variation graphs
- a -
a() :
vg::uniform_int_distribution< T >
,
vg::uniform_real_distribution< T >
accept_record() :
vg::VcfRecordFilter
add() :
vg::Packer
add_bv() :
Vectorizer
add_chain_child() :
vg::NetGraph
add_connection() :
vg::subpath_t
add_edge() :
vg::MEMClusterer::HitGraph
,
vg::VG
add_edges() :
vg::VG
add_edit() :
vg::path_mapping_t
add_exon() :
vg::Transcriptome
add_group() :
vg::StreamIndex< Message >
,
vg::StreamIndexBase
add_handle() :
vg::SubHandleGraph
add_haplotype() :
vg::PhasedGenome
add_intron_splice_junctions() :
vg::Transcriptome
add_mapping() :
vg::path_t
add_name() :
Vectorizer
add_name_mapping() :
vg::NameMapper
add_next() :
vg::subpath_t
add_node() :
vg::VG
add_nodes() :
vg::VG
add_nodes_in_range() :
vg::MinimumDistanceIndex
add_reachability_edges() :
vg::MultipathAlignmentGraph
add_snarl() :
vg::SnarlManager
add_splice_junction_edges() :
vg::Transcriptome
add_start() :
vg::multipath_alignment_t
add_start_end_markers() :
vg::VG
add_subpath() :
vg::multipath_alignment_t
add_to_number() :
bdsg::ODGI
add_transcript_splice_junctions() :
vg::Transcriptome
add_transcripts() :
vg::Transcriptome
add_transcripts_to_gbwt() :
vg::Transcriptome
add_traversals() :
vg::ExhaustiveTraversalFinder
add_unary_child() :
vg::NetGraph
add_variant() :
vg::VCFOutputCaller
add_variants() :
vg::VariantAdder
adjacent() :
vg::VG
adjacent_positions() :
vg::Mapper
advance() :
vg::io::MessageIterator
,
vg::io::ProtobufIterator< T >
,
vg::NGSSimulator
,
vg::PathBranch
advance_by_distance() :
vg::NGSSimulator
advance_on_graph() :
vg::NGSSimulator
advance_on_graph_by_distance() :
vg::NGSSimulator
advance_on_path() :
vg::NGSSimulator
advance_on_path_by_distance() :
vg::NGSSimulator
Affinity() :
vg::Genotyper::Affinity
agglomerate() :
vg::MultipathMapper
agglomerate_alignment_pairs() :
vg::MultipathMapper
agglomerate_alignments() :
vg::MultipathMapper
agglomeration_window_count() :
vg::MinimizerMapper::Minimizer
align() :
vg::Aligner
,
vg::BandedGlobalAligner< IntType >
,
vg::BaseAligner
,
vg::DozeuInterface
,
vg::Mapper
,
vg::MultipathAlignmentGraph
,
vg::QualAdjAligner
,
vg::SSWAligner
,
vg::VG
align_banded() :
vg::Mapper
align_cluster() :
vg::Mapper
align_downward() :
vg::DozeuInterface
align_global_banded() :
vg::Aligner
,
vg::GSSWAligner
,
vg::QualAdjAligner
align_global_banded_multi() :
vg::Aligner
,
vg::GSSWAligner
,
vg::QualAdjAligner
align_internal() :
vg::Aligner
,
vg::QualAdjAligner
align_maybe_flip() :
vg::Mapper
align_mem_multi() :
vg::Mapper
align_multi() :
vg::Mapper
align_multi_internal() :
vg::Mapper
align_ns() :
vg::VariantAdder
align_paired_multi() :
vg::Mapper
align_pinned() :
vg::Aligner
,
vg::DozeuInterface
,
vg::GSSWAligner
,
vg::QualAdjAligner
align_pinned_multi() :
vg::Aligner
,
vg::GSSWAligner
,
vg::QualAdjAligner
align_qual_adjusted() :
vg::VG
align_tails() :
vg::MultipathAlignmentGraph
align_to_cluster_graph_pairs() :
vg::MultipathMapper
align_to_cluster_graphs() :
vg::MultipathMapper
align_to_cluster_graphs_with_rescue() :
vg::MultipathMapper
align_to_graph() :
vg::Mapper
align_to_splice_candidates() :
vg::MultipathMapper
align_xdrop() :
vg::Aligner
,
vg::GSSWAligner
,
vg::QualAdjAligner
Aligner() :
vg::Aligner
AlignerClient() :
vg::AlignerClient
alignment() :
vg::Sampler
alignment_end_position() :
vg::Mapper
alignment_entry_to_string() :
vg::Index
alignment_pair() :
vg::Sampler
alignment_qual_score() :
vg::Genotyper
alignment_seq() :
vg::Sampler
alignment_to_a_hot() :
Vectorizer
alignment_to_custom_score() :
Vectorizer
alignment_to_graph() :
vg::Sampler
alignment_to_identity_hot() :
Vectorizer
alignment_to_onehot() :
Vectorizer
alignment_to_path() :
vg::Sampler
alignment_with_error() :
vg::Sampler
AlignmentChainModel() :
vg::AlignmentChainModel
AlignmentChainModelVertex() :
vg::AlignmentChainModelVertex
alignments_consistent() :
vg::Mapper
all_children_trivial() :
vg::SnarlManager
all_path_names() :
vg::Paths
allele() :
haplo::linear_haplo_structure::SNVvector
allele_ambiguity_log_probs() :
vg::Genotyper
AllowsAliasing() :
vg::io::BlockedGzipOutputStream
aln_to_bseq() :
vg::SRPE
AltTracebackStack() :
vg::BandedGlobalAligner< IntType >::AltTracebackStack
anchored_filter() :
vg::Filter
annotate_mapped_alignment() :
vg::Funnel
append() :
vg::Paths
,
vg::SnarlState
,
vg::VG
append_haplotype() :
vg::GenomeState
append_left() :
vg::PhasedGenome::Haplotype
append_mapping() :
vg::Paths
append_path_name() :
bdsg::PackedGraph
append_right() :
vg::PhasedGenome::Haplotype
append_step() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::MutablePathHandleGraph
,
vg::VG
append_transcript_paths() :
vg::Transcriptome
apply_aligned_base() :
vg::NGSSimulator
apply_deletion() :
vg::NGSSimulator
apply_edit() :
vg::GraphSynchronizer::Lock
apply_full_length_edit() :
vg::GraphSynchronizer::Lock
apply_haplotype_consistency_scores() :
vg::BaseMapper
apply_insertion() :
vg::NGSSimulator
apply_N_mask() :
vg::NGSSimulator
apply_ordering() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::MutableHandleGraph
,
vg::VG
apply_orientation() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::MutableHandleGraph
,
vg::VG
apply_path_ordering() :
bdsg::ODGI
apply_translation() :
vg::PathIndex
apply_translations() :
vg::PathIndex
approx_alignment_position() :
vg::Mapper
approx_distance() :
vg::Mapper
approx_fragment_length() :
vg::Mapper
approx_position() :
vg::Mapper
approx_size_of_kmer_matches() :
vg::Index
approx_sizes_of_kmer_matches() :
vg::Index
arch_is_big_endian() :
vg::endianness< IntType >
are_consecutive_nodes_in_path() :
vg::Paths
are_consistent() :
vg::MultipathMapper
as_edge_table() :
vg::Packer
as_quality_table() :
vg::Packer
as_table() :
vg::Packer
,
vg::Packers
assemble() :
vg::SRPE
at() :
vg::Option< vector< Item >, Parser >
at_next_deflection() :
vg::BandedGlobalAligner< IntType >::AltTracebackStack
at_or_after() :
vg::BitString
at_or_before() :
vg::BitString
at_position() :
vg::PathIndex
attempt_rescue() :
vg::MinimizerMapper
,
vg::MultipathMapper
attempt_rescue_for_secondaries() :
vg::MultipathMapper
attempt_unpaired_multipath_map_of_pair() :
vg::MultipathMapper
augment_from_alignment_edits() :
vg::AugmentedGraph
augment_splice_graph() :
vg::Transcriptome
average_node_quality() :
vg::Packer
avg_qual_filter() :
vg::Filter
Generated by
1.8.18