- a -

• absent : vg::Recombinator
• Adaptive : vg::Genotyper
• after : ReferenceInterval
• annotation : vg::Counts

- b -

• BAD_EDIT : vg::AlignmentValidity
• BAM : vg::MultipathAlignmentEmitter
• Basic : vg::IndexingParameters
• before : ReferenceInterval
• Bool : vg::multipath_alignment_t
• build_alignments : GBWTConfig
• build_gbwtgraph : GBWTConfig
• build_gbz : GBWTConfig
• build_gfa : GBWTConfig
• build_none : GBWTConfig
• build_paths : GBWTConfig
• build_vcf : GBWTConfig

- c -

• CHAIN : vg::ZipCode
• CHAIN_END : vg::ZipCodeTree
• CHAIN_START : vg::ZipCodeTree
• CRAM : vg::MultipathAlignmentEmitter
• CYCLIC_SNARL : vg::ZipCode

- d -

• Debug : vg::IndexingParameters
• defray : vg::Counts
• defray_all : vg::Counts
• deletion : vg::WFAAlignment
• Double : vg::multipath_alignment_t

- e -

• EDGE : vg::ZipCodeTree
• EMPTY : vg::ZipCode
• END : handlegraph::SnarlDecomposition
• excluded_feature : vg::Counts
• Exhaustive : vg::Genotyper

- f -

• filtered : vg::Counts
• first_alignment : vg::Counts
• Forward : vg::MultipathMapper
• frequent : vg::Recombinator
• full_haplotype : vg::Haplotypes::Subchain

- g -

• GAF : vg::MultipathAlignmentEmitter
• GAM : vg::MultipathAlignmentEmitter
• GAMP : vg::MultipathAlignmentEmitter
• graph_gbwtgraph : GraphHandler
• graph_gbz : GraphHandler
• graph_none : GraphHandler
• graph_path : GraphHandler
• graph_source : GraphHandler

- h -

• HashGraph : vg::IndexingParameters
• heterozygous : vg::Recombinator

- i -

• incorrectly_mapped : vg::Counts
• index_compressed : vg::GBWTHandler
• index_dynamic : vg::GBWTHandler
• index_none : vg::GBWTHandler
• InsertCol : vg::BandedGlobalAligner< IntType >
• insertion : vg::WFAAlignment
• InsertRow : vg::BandedGlobalAligner< IntType >
• invalid : haplo::linear_haplo_structure
• IRREGULAR_SNARL : vg::ZipCode

- k -

• key_gbwt_pos : vg::GAFSorterRecord
• key_hash : vg::GAFSorterRecord
• key_node_interval : vg::GAFSorterRecord

- l -

• last : vg::Counts

- m -

• Match : vg::BandedGlobalAligner< IntType >
• match : vg::WFAAlignment
• max_length : vg::Counts
• max_overhang : vg::Counts
• max_reads : vg::Counts
• merge_fast : GBWTConfig
• merge_insert : GBWTConfig
• merge_none : GBWTConfig
• merge_parallel : GBWTConfig
• min_base_qual : vg::Counts
• min_end_matches : vg::Counts
• min_mapq : vg::Counts
• min_score : vg::Counts
• min_sec_score : vg::Counts
• mismatch : vg::WFAAlignment
• mode_invalid : HaplotypesConfig
• mode_preprocess : HaplotypesConfig
• mode_sample_graph : HaplotypesConfig
• mode_sample_haplotypes : HaplotypesConfig
• mode_statistics : HaplotypesConfig

- n -

• NODE : vg::ZipCode
• NODE_COUNT : vg::ZipCodeTree
• NODE_MISSING : vg::AlignmentValidity
• NODE_TOO_SHORT : vg::AlignmentValidity
• None : vg::IndexingParameters
• normal : vg::Haplotypes::Subchain
• Null : vg::multipath_alignment_t

- o -

• OK : vg::AlignmentValidity
• overlap : ReferenceInterval

- p -

• PackedGraph : vg::IndexingParameters
• path_cover_augment : GBWTConfig
• path_cover_greedy : GBWTConfig
• path_cover_local : GBWTConfig
• path_cover_none : GBWTConfig
• prefix : vg::Haplotypes::Subchain
• present : vg::Recombinator
• preset_default : vg::Recombinator::Parameters
• preset_diploid : vg::Recombinator::Parameters
• preset_haploid : vg::Recombinator::Parameters
• proper_pair : vg::Counts

- r -

• random : vg::Counts
• read : vg::Counts
• READ_TOO_SHORT : vg::AlignmentValidity
• Reads : vg::Genotyper
• RecurseAlways : vg::GraphCaller
• RecurseNever : vg::GraphCaller
• RecurseOnFail : vg::GraphCaller
• ref_span : haplo::linear_haplo_structure
• REGULAR_SNARL : vg::ZipCode
• repeat : vg::Counts
• Representative : vg::Genotyper
• rescue_dozeu : vg::MinimizerMapper
• rescue_gssw : vg::MinimizerMapper
• rescue_none : vg::MinimizerMapper
• Reverse : vg::MultipathMapper
• ROOT_CHAIN : vg::ZipCode
• ROOT_NODE : vg::ZipCode
• ROOT_SNARL : vg::ZipCode

- s -

• S_SCAN_CHAIN : vg::ZipCodeTree::reverse_iterator
• S_SCAN_SNARL : vg::ZipCodeTree::reverse_iterator
• S_SKIP_CHAIN : vg::ZipCodeTree::reverse_iterator
• S_STACK_SNARL : vg::ZipCodeTree::reverse_iterator
• S_START : vg::ZipCodeTree::reverse_iterator
• SAM : vg::MultipathAlignmentEmitter
• SEED : vg::ZipCodeTree
• SEQ_DOES_NOT_MATCH : vg::AlignmentValidity
• SNARL_END : vg::ZipCodeTree
• SNARL_START : vg::ZipCodeTree
• snv : haplo::linear_haplo_structure
• split : vg::Counts
• START : handlegraph::SnarlDecomposition
• String : vg::multipath_alignment_t
• subsequence : vg::Counts
• suffix : vg::Haplotypes::Subchain

- t -

• TIP : handlegraph::SnarlDecomposition

- u -

• Undetermined : vg::MultipathMapper
• unmapped : vg::Counts

- v -

• verbosity_basic : vg::Haplotypes
• verbosity_debug : vg::Haplotypes
• verbosity_detailed : vg::Haplotypes
• verbosity_extra_debug : vg::Haplotypes
• verbosity_silent : vg::Haplotypes
• VG : vg::IndexingParameters

- w -

• wrong_name : vg::Counts
• wrong_refpos : vg::Counts