From 773752384cd6628e646988b9333452062dd85a50 Mon Sep 17 00:00:00 2001 From: VG Doc Bot Date: Mon, 8 Apr 2024 19:45:15 +0000 Subject: [PATCH] Commit new auto-generated docs --- alignment_8cpp.html | 2 + annotated.html | 29 +- classes.html | 642 +++++++------- find__main_8cpp.html | 1 + functions_f.html | 9 +- functions_func_f.html | 2 +- functions_func_l.html | 3 - functions_func_o.html | 30 +- functions_g.html | 25 +- functions_l.html | 6 +- functions_o.html | 24 +- functions_p.html | 14 +- functions_s.html | 4 +- functions_v.html | 10 +- functions_vars_f.html | 3 + functions_vars_g.html | 3 + gamsort__main_8cpp.html | 12 + hierarchy.html | 1015 +++++++++++----------- search/all_10.js | 934 ++++++++++---------- search/all_11.js | 54 +- search/all_12.js | 750 ++++++++-------- search/all_13.js | 1248 +++++++++++++-------------- search/all_14.js | 540 ++++++------ search/all_15.js | 186 ++-- search/all_16.js | 240 +++--- search/all_17.js | 256 +++--- search/all_18.js | 26 +- 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| 40 +- search/classes_9.js | 12 +- search/classes_a.js | 8 +- search/classes_b.js | 18 +- search/classes_c.js | 72 +- search/classes_d.js | 36 +- search/classes_e.js | 18 +- search/classes_f.js | 100 +-- search/defines_0.js | 22 +- search/defines_1.js | 2 +- search/defines_2.js | 4 +- search/defines_3.js | 6 +- search/defines_4.js | 2 +- search/defines_5.js | 122 +-- search/defines_6.js | 2 +- search/defines_7.js | 4 +- search/defines_8.js | 6 +- search/enums_0.js | 6 +- search/enums_1.js | 2 +- search/enums_2.js | 2 +- search/enums_3.js | 4 +- search/enums_4.js | 2 +- search/enums_5.js | 2 +- search/enums_6.js | 4 +- search/enums_7.js | 2 +- search/enums_8.js | 8 +- search/enums_9.js | 2 +- search/enums_a.js | 6 +- search/enums_b.js | 8 +- search/enums_c.js | 4 +- search/enums_d.js | 8 +- search/enums_e.js | 2 +- search/enums_f.js | 2 +- search/enumvalues_0.js | 26 +- search/enumvalues_1.js | 22 +- search/enumvalues_10.js | 4 +- search/enumvalues_11.js | 10 +- search/enumvalues_12.js | 10 +- search/enumvalues_13.js | 6 +- search/enumvalues_2.js | 4 +- search/enumvalues_3.js | 16 +- search/enumvalues_4.js | 8 +- search/enumvalues_5.js | 8 +- search/enumvalues_6.js | 18 +- search/enumvalues_7.js | 6 +- search/enumvalues_8.js | 28 +- search/enumvalues_9.js | 2 +- search/enumvalues_a.js | 42 +- search/enumvalues_b.js | 10 +- search/enumvalues_c.js | 4 +- search/enumvalues_d.js | 20 +- search/enumvalues_e.js | 28 +- search/enumvalues_f.js | 14 +- search/files_0.js | 48 +- search/files_1.js | 38 +- search/files_10.js | 2 +- search/files_11.js | 102 +-- search/files_12.js | 136 +-- search/files_13.js | 40 +- search/files_14.js | 6 +- search/files_15.js | 48 +- search/files_16.js | 12 +- search/files_17.js | 6 +- search/files_18.js | 4 +- search/files_2.js | 78 +- search/files_3.js | 54 +- search/files_4.js | 42 +- search/files_5.js | 42 +- search/files_6.js | 68 +- search/files_7.js | 34 +- search/files_8.js | 40 +- search/files_9.js | 16 +- search/files_a.js | 18 +- search/files_b.js | 10 +- search/files_c.js | 100 +-- search/files_d.js | 30 +- search/files_e.js | 8 +- search/files_f.js | 76 +- search/functions_0.js | 2 +- search/functions_1.js | 472 +++++----- search/functions_10.js | 492 +++++------ search/functions_11.js | 22 +- search/functions_12.js | 368 ++++---- search/functions_13.js | 714 +++++++-------- search/functions_14.js | 306 +++---- search/functions_15.js | 104 +-- search/functions_16.js | 106 +-- search/functions_17.js | 152 ++-- search/functions_18.js | 10 +- search/functions_19.js | 2 +- search/functions_1a.js | 4 +- search/functions_1b.js | 388 ++++----- search/functions_2.js | 114 +-- search/functions_3.js | 524 +++++------ search/functions_4.js | 192 ++--- search/functions_5.js | 312 +++---- search/functions_6.js | 478 +++++----- search/functions_7.js | 698 +++++++-------- search/functions_8.js | 290 +++---- search/functions_9.js | 280 +++--- search/functions_a.js | 24 +- search/functions_b.js | 46 +- search/functions_c.js | 148 ++-- search/functions_d.js | 500 +++++------ search/functions_e.js | 150 ++-- search/functions_f.js | 122 +-- search/namespaces_0.js | 6 +- search/namespaces_1.js | 10 +- search/namespaces_2.js | 2 +- search/namespaces_3.js | 10 +- search/namespaces_4.js | 4 +- search/namespaces_5.js | 2 +- search/related_0.js | 2 +- search/related_1.js | 4 +- search/related_2.js | 4 +- search/related_3.js | 4 +- search/related_4.js | 6 +- search/related_5.js | 6 +- search/related_6.js | 2 +- search/related_7.js | 2 +- search/typedefs_0.js | 2 +- search/typedefs_1.js | 12 +- search/typedefs_10.js | 24 +- search/typedefs_11.js | 14 +- search/typedefs_12.js | 10 +- search/typedefs_13.js | 2 +- search/typedefs_2.js | 24 +- search/typedefs_3.js | 8 +- search/typedefs_4.js | 10 +- search/typedefs_5.js | 2 +- search/typedefs_6.js | 10 +- search/typedefs_7.js | 14 +- search/typedefs_8.js | 14 +- search/typedefs_9.js | 4 +- search/typedefs_a.js | 2 +- search/typedefs_b.js | 24 +- search/typedefs_c.js | 8 +- search/typedefs_d.js | 6 +- search/typedefs_e.js | 24 +- search/typedefs_f.js | 14 +- search/variables_0.js | 46 +- search/variables_1.js | 130 +-- search/variables_10.js | 316 +++---- search/variables_11.js | 30 +- search/variables_12.js | 220 ++--- search/variables_13.js | 332 +++---- search/variables_14.js | 174 ++-- search/variables_15.js | 60 +- search/variables_16.js | 52 +- search/variables_17.js | 62 +- search/variables_18.js | 6 +- search/variables_2.js | 116 +-- search/variables_3.js | 202 ++--- search/variables_4.js | 250 +++--- search/variables_5.js | 142 +-- search/variables_6.js | 145 ++-- search/variables_7.js | 157 ++-- search/variables_8.js | 92 +- search/variables_9.js | 168 ++-- search/variables_a.js | 8 +- search/variables_b.js | 22 +- search/variables_c.js | 110 +-- search/variables_d.js | 516 +++++------ search/variables_e.js | 206 ++--- search/variables_f.js | 116 +-- structGafFile-members.html | 83 ++ structGafFile.html | 121 +++ structcompare__gaf-members.html | 82 ++ structcompare__gaf.html | 127 +++ structgreater__gaffile-members.html | 82 ++ structgreater__gaffile.html | 127 +++ 230 files changed, 13940 insertions(+), 13269 deletions(-) create mode 100644 structGafFile-members.html create mode 100644 structGafFile.html create mode 100644 structcompare__gaf-members.html create mode 100644 structcompare__gaf.html create mode 100644 structgreater__gaffile-members.html create mode 100644 structgreater__gaffile.html diff --git a/alignment_8cpp.html b/alignment_8cpp.html index 37b6584147f..f57b80a6047 100644 --- a/alignment_8cpp.html +++ b/alignment_8cpp.html @@ -76,7 +76,9 @@
#include "alignment.hpp"
#include "vg/io/gafkluge.hpp"
#include "annotation.hpp"
+#include <vg/io/stream.hpp>
#include <sstream>
+#include <chrono>
diff --git a/annotated.html b/annotated.html index 304562910a8..624ca420c88 100644 --- a/annotated.html +++ b/annotated.html @@ -574,19 +574,22 @@ - - - - - - - - - - - - - + + + + + + + + + + + + + + + +

Namespaces

 CGBWTConfig
 CGiraffeMainOptionsOptions struct for options for the Giraffe driver (i.e. this file)
 CGraphHandler
 CHaplotypesConfig
 ChFILE_backend
 Cj2pb_error
 Cjob_type
 Cjson_autoptr
 CMappingRun
 CPruningParameters
 CReferenceInterval
 CScoringOptionsOptions struct for scoring-related parameters. Defaults are in aligner.hpp
 CVectorizer
 Ccompare_gaf
 CGafFile
 CGBWTConfig
 CGiraffeMainOptionsOptions struct for options for the Giraffe driver (i.e. this file)
 CGraphHandler
 Cgreater_gaffile
 CHaplotypesConfig
 ChFILE_backend
 Cj2pb_error
 Cjob_type
 Cjson_autoptr
 CMappingRun
 CPruningParameters
 CReferenceInterval
 CScoringOptionsOptions struct for scoring-related parameters. Defaults are in aligner.hpp
 CVectorizer
diff --git a/classes.html b/classes.html index 6f5482624e2..15bc2c14b38 100644 --- a/classes.html +++ b/classes.html @@ -71,666 +71,670 @@
  a  
Filter (vg)    -ShuffledPairs::iterator (vg)    -HaplotypePartitioner::Parameters (vg)    -state_hash (vg)    +Funnel::Item (vg)    +Recombinator::Parameters (vg)    +Recombinator::Statistics (vg)    Funnel::FilterPerformance (vg)    -PhasedGenome::iterator (vg)    +ShuffledPairs::iterator (vg)    Path (vg)    -Recombinator::Statistics (vg)    +step_handle_t (handlegraph)    AbstractReadSampler (vg)    FixedGenotypePriorCalculator (vg)    PathForEachSocket::iterator (handlegraph)    path_handle_t (handlegraph)    -step_handle_t (handlegraph)    +StrandSplitGraph (vg)    Genotyper::Affinity (vg)    FlagArgSpec (vg::subcommand)    -iterator_traits< vg::PhasedGenome::iterator > (std)    +PhasedGenome::iterator (vg)    path_mapping_t (vg)    -StrandSplitGraph (vg)    +streaminbuf (vg::io)    AliasGraph (vg)    FlatFileBackTranslation (vg)    -IncrementalSubgraph::IterFCmp (vg)    +iterator_traits< vg::PhasedGenome::iterator > (std)    path_t (vg)    -streaminbuf (vg::io)    +StreamIndex (vg)    Aligner (vg)    FlowCaller (vg)    -
  j  
- +IncrementalSubgraph::IterFCmp (vg)    PathBasedTraversalFinder (vg)    -StreamIndex (vg)    +StreamIndexBase (vg)    AlignerClient (vg)    FlowSort (vg)    +
  j  
+ PathBranch (vg)    -StreamIndexBase (vg)    +streamistream (vg::io)    Alignment (vg)    FlowTraversalFinder (vg)    -j2pb_error    PathChunker (vg)    -streamistream (vg::io)    +StreamMultiplexer (vg::io)    alignment_index_t (vg)    FragmentLengthDistribution (vg)    -job_type    +j2pb_error    PathComponentIndex (vg)    -StreamMultiplexer (vg::io)    +StreamSorter (vg)    AlignmentChainModel (vg)    FragmentLengthStatistics (vg)    -JobSchedule (vg)    +job_type    PathForEachSocket (handlegraph)    -StreamSorter (vg)    +string_hash_map (vg)    AlignmentChainModelVertex (vg)    Funnel (vg)    -JoinedSpliceGraph (vg)    +JobSchedule (vg)    PathHandleGraph (handlegraph)    -string_hash_map (vg)    +string_hash_set (vg)    AlignmentEmitter (vg::io)   
  g  
-json_autoptr    +JoinedSpliceGraph (vg)    PathIndex (vg)    -string_hash_set (vg)    +Haplotypes::Subchain (vg)    AlignmentValidity (vg)    -JSONStreamHelper (vg::io)    +json_autoptr    MatchPos::PathList (vg)    HaplotypePartitioner::Subchain (vg)    BandedGlobalAligner::AltTracebackStack (vg)    GafAlignmentEmitter (vg::io)    -
  k  
- +JSONStreamHelper (vg::io)    PathMetadata (handlegraph)    -Haplotypes::Subchain (vg)    +Subcommand (vg::subcommand)    Anchor (vg::algorithms)    -GAFOutputCaller (vg)    +GafFile    +
  k  
+ PathNode (vg)    -Subcommand (vg::subcommand)    +SubgraphOverlay (vg)    Annotation (vg)    -GafRecord (gafkluge)    -kff_recoding_t (vg)    +GAFOutputCaller (vg)    PathOrientedDistanceMeasurer (vg)    -SubgraphOverlay (vg)    +SubHandleGraph (vg)    AppendHaplotypeCommand (vg)    -GafStep (gafkluge)    -kmer_t (vg)    +GafRecord (gafkluge)    +kff_recoding_t (vg)    PathPositionHandleGraph (handlegraph)    -SubHandleGraph (vg)    +SubHandleGraph (handlegraph::algorithms)    ArgSpec (vg::subcommand)    -GaplessExtender (vg)    -kmer_t (vg::algorithms)    +GafStep (gafkluge)    +kmer_t (vg)    PathRestrictedTraversalFinder (vg)    -SubHandleGraph (handlegraph::algorithms)    +Subpath (vg)    AugmentedGraph (vg)    -GaplessExtension (vg)    -KmerMatch (vg)    +GaplessExtender (vg)    +kmer_t (vg::algorithms)    Paths (vg)    -Subpath (vg)    +subpath_t (vg)   
  b  
-gbwt_thread_t (haplo)    -KmerPosition (vg)    +GaplessExtension (vg)    +KmerMatch (vg)    PathSubgraph (vg)    -subpath_t (vg)    +SummaryStatistics (vg)    -GBWTConfig    -
  l  
- +gbwt_thread_t (haplo)    +KmerPosition (vg)    PathSubgraphOverlay (vg)    -SummaryStatistics (vg)    +Support (vg)    BandedGlobalAligner::BABuilder (vg)    -GBWTHandler (vg)    +GBWTConfig    +
  l  
+ PathTraversalFinder (vg)    -Support (vg)    +SupportAugmentedGraph (vg)    BackTranslatingAlignmentEmitter (vg)    -GBWTScoreProvider (haplo)    -LazyRNG (vg)    +GBWTHandler (vg)    PhasedGenome (vg)    -SupportAugmentedGraph (vg)    +SupportBasedSnarlCaller (vg)    BandedGlobalAligner::BAMatrix (vg)    -GBWTTraversalFinder (vg)    -LegacyCaller (vg)    +GBWTScoreProvider (haplo)    +LazyRNG (vg)    PhaseUnfolder (vg)    -SupportBasedSnarlCaller (vg)    +SupportRestrictedTraversalFinder (vg)    BandedGlobalAligner (vg)    -GBZGraph (vg)    -linear_haplo_structure (haplo)    +GBWTTraversalFinder (vg)    +LegacyCaller (vg)    Pictographs (vg)    -SupportRestrictedTraversalFinder (vg)    +SurjectingAlignmentEmitter (vg)    BaseAligner (vg)    -GenomeState (vg)    -LinearScoreProvider (haplo)    +GBZGraph (vg)    +linear_haplo_structure (haplo)    Pileup (vg)    -SurjectingAlignmentEmitter (vg)    +Surjector (vg)    BaseArgSpec (vg::subcommand)    -GenomeStateCommand (vg)    -linear_haplo_structure::linearUnrepresentable (haplo)    +GenomeState (vg)    +LinearScoreProvider (haplo)    VG::Plan (vg)    -Surjector (vg)    +SwapHaplotypesCommand (vg)    BaseMapper (vg)    -Genotype (vg)    -Recombinator::LocalHaplotype (vg)    +GenomeStateCommand (vg)    +linear_haplo_structure::linearUnrepresentable (haplo)    PoissonSupportSnarlCaller::PoissonCallInfo (vg)    -SwapHaplotypesCommand (vg)    +
  t  
+ BaseOption (vg)    -GenotypeLikelihoodCalculator (vg)    -LocationSupport (vg)    +Genotype (vg)    +Recombinator::LocalHaplotype (vg)    PoissonSupportSnarlCaller (vg)    -
  t  
- BaseOptionGroup (vg::subcommand)    -GenotypePriorCalculator (vg)    -GraphSynchronizer::Lock (vg)    +GenotypeLikelihoodCalculator (vg)    +LocationSupport (vg)    Position (vg)    +Registry::Tables (vg::io)    BasePileup (vg)    -Genotyper (vg)    -Locus (vg)    +GenotypePriorCalculator (vg)    +GraphSynchronizer::Lock (vg)    position_t (vg)    -Registry::Tables (vg::io)    +TargetValueSearch (vg)    BaseValuation (vg::subcommand)    -GFADuplicatePathError (vg::algorithms)    -
  m  
- +Genotyper (vg)    +Locus (vg)    PositionIDScanner (vg)    -TargetValueSearch (vg)    +Watchdog::thread_state_t (vg)    BBEdgeHash (vg)    -GFAFormatError (vg::algorithms)    +GFADuplicatePathError (vg::algorithms)    +
  m  
+ Preset (vg::subcommand)    -Watchdog::thread_state_t (vg)    +TickChainLink (vg::subcommand)    BenchmarkResult (vg)    -GFAHandleGraph (vg)    -Mapper (vg)    +GFAFormatError (vg::algorithms)    ProblemDumpExplainer (vg)    -TickChainLink (vg::subcommand)    +TipAnchoredMaxDistance (vg)    BitString (vg)    -GFAIDMapInfo (vg::algorithms)    -Mapping (vg)    +GFAHandleGraph (vg)    +Mapper (vg)    Progressive (vg)    -TipAnchoredMaxDistance (vg)    +Haplotypes::TopLevelChain (vg)    BitStringTree (vg)    -GFAParser (vg::algorithms)    -mapping_t (vg)    +GFAIDMapInfo (vg::algorithms)    +Mapping (vg)    ProtobufEmitter (vg::io)    -Haplotypes::TopLevelChain (vg)    +TracedScore (vg::algorithms)    BlockedGzipInputStream (vg::io)    -GFFReader (vg)    -MappingHash (vg)    +GFAParser (vg::algorithms)    +mapping_t (vg)    ProtobufIterator (vg::io)    -TracedScore (vg::algorithms)    +Transcript (vg)    BlockedGzipOutputStream (vg::io)    -GFFRecord (vg)    -MappingRun    +GFFReader (vg)    +MappingHash (vg)    PruningParameters    -Transcript (vg)    +Transcriptome (vg)    BoolReturningWrapper (handlegraph)    -GiraffeMainOptions    -NGSSimulator::MarkovDistribution (vg)    +GFFRecord (vg)    +MappingRun   
  q  
-Transcriptome (vg)    +TranscriptPath (vg)    BoolReturningWrapper< Iteratee, false > (handlegraph)    -Graph (vg::algorithms)    -MatchPos (vg)    -TranscriptPath (vg)    +GiraffeMainOptions    +NGSSimulator::MarkovDistribution (vg)    +Translation (vg)    BoolReturningWrapper< Iteratee, true > (handlegraph)    -Graph (vg)    -MaximalExactMatch (vg)    +Graph (vg::algorithms)    +MatchPos (vg)    QualAdjAligner (vg)    -Translation (vg)    +Translator (vg)    BREAKPOINT (vg)    -DozeuInterface::graph_pos_s (vg)    -MCMCCaller (vg)    +Graph (vg)    +MaximalExactMatch (vg)    QualAdjXdropAligner (vg)    -Translator (vg)    +TraversalFinder (vg)    BuildableSnarlDecomposition (handlegraph)    -GraphCaller (vg)    -MCMCGenotyper (vg)    +DozeuInterface::graph_pos_s (vg)    +MCMCCaller (vg)   
  r  
-TraversalFinder (vg)    +TraversalSupportCalculator (vg)   
  c  
-GraphHandler    -MEMAccelerator (vg)    -TraversalSupportCalculator (vg)    +GraphCaller (vg)    +MCMCGenotyper (vg)    +TraversalSupportFinder (vg)    -GraphSynchronizer (vg)    -MEMChainModel (vg)    +GraphHandler    +MEMAccelerator (vg)    Range (vg)    -TraversalSupportFinder (vg)    +Tree (vg)    CachedPackedTraversalSupportFinder (vg)    -GreedyMinDistanceClusterer (vg)    -MEMChainModelVertex (vg)    +GraphSynchronizer (vg)    +MEMChainModel (vg)    RangeArgSpec (vg::subcommand)    -Tree (vg)    +BitStringTree::TreeNode (vg)    IndexedVG::CacheEntry (vg)    -GroupedOptionGroup (vg::subcommand)    -MEMClusterer (vg)    +greater_gaffile    +MEMChainModelVertex (vg)    RankedHandleGraph (handlegraph)    TreeNode (vg)    CactusSide (vg)    -FlowSort::Growth (vg)    -MemoizingGraph (vg)    +GreedyMinDistanceClusterer (vg)    +MEMClusterer (vg)    RareVariantSimplifier (vg)    -BitStringTree::TreeNode (vg)    +TreeSubgraph (vg)    CactusSnarlFinder (vg)    -GSSWAligner (vg)    -IntegratedSnarlFinder::MergedAdjacencyGraph (vg)    +GroupedOptionGroup (vg::subcommand)    +MemoizingGraph (vg)    RatioSupportSnarlCaller (vg)    -TreeSubgraph (vg)    +TriviallySerializable (handlegraph)    SnarlCaller::CallInfo (vg)    -
  h  
- -MessageEmitter (vg::io)    -read_alignment_index_t (vg)    -TriviallySerializable (handlegraph)    +FlowSort::Growth (vg)    +IntegratedSnarlFinder::MergedAdjacencyGraph (vg)    +read_alignment_index_t (vg)    +TrivialTraversalFinder (vg)    NestedFlowCaller::CallRecord (vg)    -MessageIterator (vg::io)    +GSSWAligner (vg)    +MessageEmitter (vg::io)    ReadFilter (vg)    -TrivialTraversalFinder (vg)    +truncated_normal_distribution (vg)    ChainIterator (vg)    -handle_t (handlegraph)    -MinDistanceClusterer (vg)    +
  h  
+ +MessageIterator (vg::io)    ReadMasker (vg)    -truncated_normal_distribution (vg)    +TSVAlignmentEmitter (vg::io)    SnarlDistanceIndexClusterer::Cluster (vg)    -HandleGraph (handlegraph)    -MinimizerMapper::Minimizer (vg)    +MinDistanceClusterer (vg)    ReadRestrictedTraversalFinder (vg)    -TSVAlignmentEmitter (vg::io)    +TVSClusterer (vg)    SnarlDistanceIndexClusterer::ClusterHead (vg)    -HandleGraphNodeSet (vg)    -MinimizerMapper (vg)    +handle_t (handlegraph)    +MinimizerMapper::Minimizer (vg)    RebuildJob (vg)    -TVSClusterer (vg)    +
  u  
+ SnarlDistanceIndexClusterer::ClusteringProblem (vg)    -HandleGraphSnarlFinder (vg)    -MIPayload (vg)    +HandleGraph (handlegraph)    +MinimizerMapper (vg)    RebuildParameters (vg)    -
  u  
- Colors (vg)    -Handler (vg::temp_file)    -MIPayloadValues (vg)    +HandleGraphNodeSet (vg)    +MIPayload (vg)    Recombinator (vg)    +uniform_int_distribution (vg)    + +compare_gaf    +HandleGraphSnarlFinder (vg)    +MIPayloadValues (vg)    +RecombinatorHaplotype (vg)    +uniform_real_distribution (vg)    CompletedTranscriptPath (vg)    -Handler (xg::temp_file)    +Handler (vg::temp_file)    MSAConverter (vg)    -RecombinatorHaplotype (vg)    -uniform_int_distribution (vg)    +ReferenceInterval    +
  v  
+ ComponentMinDistanceClusterer (vg)    -haplo_DP (haplo)    +Handler (xg::temp_file)    multipath_alignment_t (vg)    -ReferenceInterval    -uniform_real_distribution (vg)    +Region (vg)    Configurable (vg)    -haplo_DP_column (haplo)    +haplo_DP (haplo)    MultipathAlignment (vg)    -Region (vg)    -
  v  
- +RegionExpander (vg)    +Valuation (vg::subcommand)    ConfigurableParser (vg)    -haplo_DP_rectangle (haplo)    +haplo_DP_column (haplo)    MultipathAlignmentEmitter (vg)    -RegionExpander (vg)    +Registry (vg::io)    +ValueArgSpec (vg::subcommand)    Connection (vg)    -PhasedGenome::Haplotype (vg)    +haplo_DP_rectangle (haplo)    MultipathAlignmentGraph (vg)    -Registry (vg::io)    -Valuation (vg::subcommand)    +ReplaceLocalHaplotypeCommand (vg)    +VariantAdder (vg)    connection_t (vg)    -HaplotypeIndexer (vg)    +PhasedGenome::Haplotype (vg)    MultipathMapper (vg)    -ReplaceLocalHaplotypeCommand (vg)    -ValueArgSpec (vg::subcommand)    +ReplaceSnarlHaplotypeCommand (vg)    +VcfBuffer (vg)    ConsistencyCalculator (vg)    -PhasedGenome::HaplotypeNode (vg)    +HaplotypeIndexer (vg)    MultipathProblem (vg)    -ReplaceSnarlHaplotypeCommand (vg)    -VariantAdder (vg)    +RepresentativeTraversalFinder (vg)    +VCFGenotyper (vg)    VectorView::const_iterator (vg)    -HaplotypePartitioner (vg)    +PhasedGenome::HaplotypeNode (vg)    MutableHandleGraph (handlegraph)    -RepresentativeTraversalFinder (vg)    -VcfBuffer (vg)    +return_type_of (handlegraph)    +VCFOutputCaller (vg)    ConstructedChunk (vg)    -Haplotypes (vg)    +HaplotypePartitioner (vg)    MutablePathDeletableHandleGraph (handlegraph)    -return_type_of (handlegraph)    -VCFGenotyper (vg)    +return_type_of< Returns(*)(Args...)> (handlegraph)    +VcfRecordConverter (vg)    Constructor (vg)    -HaplotypesConfig    +Haplotypes (vg)    MutablePathHandleGraph (handlegraph)    -return_type_of< Returns(*)(Args...)> (handlegraph)    -VCFOutputCaller (vg)    +return_type_of< Returns(Owner::*)(Args...) const > (handlegraph)    +VcfRecordFilter (vg)    ContractingGraph (vg)    -hash< const vg::Snarl > (std)    +HaplotypesConfig    MutablePathMetadata (handlegraph)    -return_type_of< Returns(Owner::*)(Args...) const > (handlegraph)    -VcfRecordConverter (vg)    +return_type_of< Returns(Owner::*)(Args...)> (handlegraph)    +VCFTraversalFinder (vg)    ConvertedHashGraph (vg::io)    -hash< handlegraph::edge_t > (std)    +hash< const vg::Snarl > (std)    MutablePathMutableHandleGraph (handlegraph)    -return_type_of< Returns(Owner::*)(Args...)> (handlegraph)    -VcfRecordFilter (vg)    +ReverseGraph (vg)    +VectorizableHandleGraph (handlegraph)    count_back_inserter (vg)    -hash< handlegraph::handle_t > (std)    +hash< handlegraph::edge_t > (std)   
  n  
-ReverseGraph (vg)    -VCFTraversalFinder (vg)    +RewindPlanException (vg)    +Vectorizer    Counts (vg)    -hash< handlegraph::net_handle_t > (std)    -RewindPlanException (vg)    -VectorizableHandleGraph (handlegraph)    +hash< handlegraph::handle_t > (std)    +RRMemo (haplo::haploMath)    +VectorView (vg)   
  d  
-hash< handlegraph::path_handle_t > (std)    +hash< handlegraph::net_handle_t > (std)    NamedNodeBackTranslation (handlegraph)    -RRMemo (haplo::haploMath)    -Vectorizer    - -hash< handlegraph::step_handle_t > (std)    -NameMapper (vg)   
  s  
-VectorView (vg)    +VectorViewInverse (vg)    + +hash< handlegraph::path_handle_t > (std)    +NameMapper (vg)    +Version (vg)    DagifiedGraph (vg)    -hash< pair< A, B > > (std)    +hash< handlegraph::step_handle_t > (std)    NestedCachedPackedTraversalSupportFinder (vg)    -VectorViewInverse (vg)    +Sampler (vg)    +VG (vg)    Deconstructor (vg)    -hash< std::tuple< TT... > > (std)    +hash< pair< A, B > > (std)    NestedFlowCaller (vg)    -Sampler (vg)    -Version (vg)    +WFATree::ScoreProperties (vg)    +VGAlignmentEmitter (vg::io)    BandedGlobalAligner::AltTracebackStack::Deflection (vg)    -hash< vg::NodeSide > (std)    +hash< std::tuple< TT... > > (std)    NestedTraversalFinder (vg)    -WFATree::ScoreProperties (vg)    -VG (vg)    +ScoreProvider (haplo)    +VGIndexes (vg)    DeletableHandleGraph (handlegraph)    -hash< vg::NodeTraversal > (std)    +hash< vg::NodeSide > (std)    net_handle_t (handlegraph)    -ScoreProvider (haplo)    -VGAlignmentEmitter (vg::io)    +ScoringOptions    +VGset (vg)    DeleteHaplotypeCommand (vg)    -Genotyper::hash_ambiguous_allele_set (vg)    +hash< vg::NodeTraversal > (std)    NetGraph (vg)    -ScoringOptions    -VGIndexes (vg)    +SnarlDistanceIndexClusterer::Seed (vg)    +Visit (vg)    DeletionAligner (vg)    -hash_map (vg)    +Genotyper::hash_ambiguous_allele_set (vg)    NGSSimulator (vg)    -SnarlDistanceIndexClusterer::Seed (vg)    -VGset (vg)    +SnarlDistanceIndexClusterer::SeedCache (vg)    +Viz (vg)    DiagramExplainer (vg)    -hash_map< K *, V > (vg)    +hash_map (vg)    NoAlignmentInBandException (vg)    -SnarlDistanceIndexClusterer::SeedCache (vg)    -Visit (vg)    +SeqComplexity (vg)    +VPKG (vg::io)    DinucleotideMachine (vg)    -Genotyper::hash_node_traversal (vg)    +hash_map< K *, V > (vg)    Node (vg::algorithms)    -SeqComplexity (vg)    -Viz (vg)    +Serializable (handlegraph)    +
  w  
+ discrete_distribution (vg)    -Genotyper::hash_oriented_edge (vg)    +Genotyper::hash_node_traversal (vg)    Node (vg)    -Serializable (handlegraph)    -VPKG (vg::io)    +SerializableHandleGraph (handlegraph)    DistanceHeuristic (vg)    -hash_set (vg)    +Genotyper::hash_oriented_edge (vg)    NodePileup (vg)    -SerializableHandleGraph (handlegraph)    -
  w  
- +ShuffledPairs (vg)    +walk_t (vg::algorithms)    DotDumpExplainer (vg)    -hash_set< K * > (vg)    +hash_set (vg)    NodeSide (vg)    -ShuffledPairs (vg)    +SimpleConsistencyCalculator (vg)    +wang_hash (vg)    DozeuInterface (vg)    -hDP_gbwt_graph_accessor (haplo)    +hash_set< K * > (vg)    NodeTraversal (vg)    -SimpleConsistencyCalculator (vg)    -walk_t (vg::algorithms)    +SimpleTraversalSupportCalculator (vg)    +wang_hash< handle_t > (vg)    DozeuPinningOverlay (vg)    -Haplotypes::Header (vg)    +hDP_gbwt_graph_accessor (haplo)    normal_distribution (vg)    -SimpleTraversalSupportCalculator (vg)    -wang_hash (vg)    +SizeLimitExceededException (vg)    +wang_hash< handlegraph::net_handle_t > (vg)    MEMClusterer::DPScoreComparator (vg)    -hFILE_backend    +Haplotypes::Header (vg)    NullAlignmentEmitter (vg::io)    -SizeLimitExceededException (vg)    -wang_hash< handle_t > (vg)    +SmallBitset (vg)    +wang_hash< NodeSide > (vg)   
  e  
-hFILE_cppstream (vg::io)    +hFILE_backend    NullClusterer (vg)    -SmallBitset (vg)    -wang_hash< handlegraph::net_handle_t > (vg)    +SmallSnarlSimplifier (vg)    +wang_hash< NodeTraversal > (vg)    -MEMClusterer::HitEdge (vg)    +hFILE_cppstream (vg::io)    NullMaskingGraph (vg)    -SmallSnarlSimplifier (vg)    -wang_hash< NodeSide > (vg)    +Snarl (vg)    +wang_hash< path_handle_t > (vg)    Edge (vg::algorithms)    -MEMClusterer::HitGraph (vg)    +MEMClusterer::HitEdge (vg)    number_bool_packing (handlegraph)    -Snarl (vg)    -wang_hash< NodeTraversal > (vg)    +NestedCachedPackedTraversalSupportFinder::snarl_less (vg)    +wang_hash< std::pair< A, B > > (vg)    Edge (vg)    -MEMClusterer::HitNode (vg)    +MEMClusterer::HitGraph (vg)   
  o  
-NestedCachedPackedTraversalSupportFinder::snarl_less (vg)    -wang_hash< path_handle_t > (vg)    +SnarlCaller (vg)    +wang_hash< T * > (vg)    EdgePileup (vg)    -HTSAlignmentEmitter (vg)    -SnarlCaller (vg)    -wang_hash< std::pair< A, B > > (vg)    +MEMClusterer::HitNode (vg)    +SnarlDecomposition (handlegraph)    +wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type > (vg)    Edit (vg)    -HTSWriter (vg)    +HTSAlignmentEmitter (vg)    Option (vg)    -SnarlDecomposition (handlegraph)    -wang_hash< T * > (vg)    +SnarlDistanceIndexClusterer (vg)    +Watchdog (vg)    edit_t (vg)    -
  i  
- +HTSWriter (vg)    Option< vector< Item >, Parser > (vg)    -SnarlDistanceIndexClusterer (vg)    -wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type > (vg)    +SnarlFinder (vg)    +FlowSort::WeightedGraph (vg)    EditedTranscriptPath (vg)    +
  i  
+ OptionGroup (vg::subcommand)    -SnarlFinder (vg)    -Watchdog (vg)    +SnarlGraph (vg)    +WFAAlignment (vg)    endianness (vg)    -IdentityOverlay (vg)    OptionInterface (vg)    -SnarlGraph (vg)    -FlowSort::WeightedGraph (vg)    +SnarlManager (vg)    +WFAExtender (vg)    WFAExtender::ErrorModel (vg)    -IDScanner (vg)    +IdentityOverlay (vg)    OptionValueParser (vg)    -SnarlManager (vg)    -WFAAlignment (vg)    +SnarlMinDistance (vg)    +WFANode (vg)    WFAExtender::ErrorModel::Event (vg)    -IncrementalSubgraph (vg)    +IDScanner (vg)    OptionValueParser< vector< Item > > (vg)    -SnarlMinDistance (vg)    -WFAExtender (vg)    +SnarlOrientedDistanceMeasurer (vg)    +WFAPoint (vg)    ExhaustiveTraversalFinder (vg)    -IncrementIter (vg)    +IncrementalSubgraph (vg)    DozeuInterface::OrderedGraph (vg)    -SnarlOrientedDistanceMeasurer (vg)    -WFANode (vg)    +SnarlManager::SnarlRecord (vg)    +WFATree (vg)    Exon (vg)    -IndexedVG (vg)    +IncrementIter (vg)    OrientedDistanceClusterer (vg)    -SnarlManager::SnarlRecord (vg)    -WFAPoint (vg)    +SnarlState (vg)    +WideningPRNG (vg)    ExpandingOverlayGraph (handlegraph)    -IndexFile (vg)    +IndexedVG (vg)    OrientedDistanceMeasurer (vg)    -SnarlState (vg)    -WFATree (vg)    +SnarlTraversal (vg)    +WindowedVcfBuffer (vg)    Explainer (vg)    -IndexingParameters (vg)    +IndexFile (vg)   
  p  
-SnarlTraversal (vg)    -WideningPRNG (vg)    +SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild (vg)    +WrappingPositionScanner (vg)    ExtraNodeGraph (vg)    -IndexingPlan (vg)    -SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild (vg)    -WindowedVcfBuffer (vg)    +IndexingParameters (vg)    +SnarlDistanceIndexClusterer::SnarlTreeNodeProblem (vg)    +
  x  
+
  f  
-IndexRecipe (vg)    +IndexingPlan (vg)    PackedTraversalSupportFinder (vg)    -SnarlDistanceIndexClusterer::SnarlTreeNodeProblem (vg)    -WrappingPositionScanner (vg)    +linear_haplo_structure::SNVvector (haplo)    -IndexRegistry (vg)    +IndexRecipe (vg)    Packer (vg)    -linear_haplo_structure::SNVvector (haplo)    -
  x  
- +SourceSinkOverlay (vg)    +XdropAligner (vg)    IncrementalSubgraph::FCmp (vg)    -InsertHaplotypeCommand (vg)    +IndexRegistry (vg)    Packers (vg)    -SourceSinkOverlay (vg)    +SparseUnionFind (vg)    +XG (xg)    fdinbuf (vg::io)    -InsufficientInputException (vg)    +InsertHaplotypeCommand (vg)    Funnel::PaintableSpace (vg)    -SparseUnionFind (vg)    -XdropAligner (vg)    +SplicedHTSAlignmentEmitter (vg)    +XGFormatError (xg)    fdistream (vg::io)    -int_itvl_t (haplo)    +InsufficientInputException (vg)    pair_hash_map (vg)    -SplicedHTSAlignmentEmitter (vg)    -XG (xg)    +SpliceRegion (vg)    +XGPath (xg)    fdostream (vg::io)    -IntegratedSnarlFinder (vg)    +int_itvl_t (haplo)    pair_hash_set (vg)    -SpliceRegion (vg)    -XGFormatError (xg)    - +SpliceStats (vg)    + fdoutbuf (vg::io)    -is_instantiation_of (vg)    +IntegratedSnarlFinder (vg)    PairedEndMapper (vg)    -SpliceStats (vg)    -XGPath (xg)    - +SSWAligner (vg)    + FeatureSet::Feature (vg)    -is_instantiation_of< Predicate< PredicateArgs... >, Predicate > (vg)    +is_instantiation_of (vg)    ParallelKFFReader (vg)    -SSWAligner (vg)    +Funnel::Stage (vg)    FeatureSet (vg)    -Funnel::Item (vg)    -Recombinator::Parameters (vg)    -Funnel::Stage (vg)    +is_instantiation_of< Predicate< PredicateArgs... >, Predicate > (vg)    +HaplotypePartitioner::Parameters (vg)    +state_hash (vg)    diff --git a/find__main_8cpp.html b/find__main_8cpp.html index 10a2744546f..8f4488df4c2 100644 --- a/find__main_8cpp.html +++ b/find__main_8cpp.html @@ -89,6 +89,7 @@ #include "../algorithms/extract_connecting_graph.hpp"
#include "../algorithms/walk.hpp"
#include <bdsg/overlays/overlay_helper.hpp>
+#include <htslib/hts.h>
#include <unistd.h>
#include <getopt.h>
diff --git a/functions_f.html b/functions_f.html index 03370d2b330..85487b0fa7c 100644 --- a/functions_f.html +++ b/functions_f.html @@ -133,6 +133,9 @@

- f -

+ + + + + + + +

+Classes

struct  compare_gaf
 
struct  GafFile
 
struct  greater_gaffile
 
diff --git a/hierarchy.html b/hierarchy.html index d085ceb1aa0..24a194ee137 100644 --- a/hierarchy.html +++ b/hierarchy.html @@ -127,512 +127,515 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Functions

void help_gamsort (char **argv)
 Cvg::SnarlDistanceIndexClusterer::ClusterHead
 Cvg::SnarlDistanceIndexClusterer::ClusteringProblem
 Cvg::Colors
 Cvg::Configurable
 Cvg::ConfigurableParser
 Cvg::ConnectionAn edge in a MultipathAlignment between Subpaths that may not be contiguous in the graph
 Cvg::connection_t
 ►Cvg::ConsistencyCalculator
 Cvg::VectorView< Item >::const_iteratorRandom access iterator
 Cvg::ConstructedChunk
 Cvg::ContractingGraph
 Cvg::count_back_inserter< T >
 Cvg::Counts
 Cvg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
 Cvg::DeletionAligner
 Cvg::DinucleotideMachine
 Cvg::discrete_distribution< T >We provide a partial discrete_distribution implementation that is just the parts we need
 ►Cvg::DistanceHeuristic
 ►Cvg::DozeuInterface
 Cvg::MEMClusterer::DPScoreComparator
 Cvg::algorithms::Edge
 Cvg::Edge
 Cvg::EdgePileupKeep pileup-like record for reads that span edges
 Cvg::Edit
 Cvg::edit_t
 Cvg::endianness< IntType >
 Cvg::WFAExtender::ErrorModel
 Cvg::WFAExtender::ErrorModel::Event
 ►Cexception
 Cvg::Exon
 ►Cvg::Explainer
 ►Cfalse_type
 Cvg::IncrementalSubgraph::FCmp
 Cvg::FeatureSet::Feature
 Cvg::FeatureSet
 Cvg::Filter
 Cvg::Funnel::FilterPerformance
 Cvg::FlowSort
 Cvg::FragmentLengthDistribution
 Cvg::FragmentLengthStatistics
 Cvg::Funnel
 ►Cvg::GAFOutputCaller
 Cgafkluge::GafRecord
 Cgafkluge::GafStep
 Cvg::GaplessExtender
 Cvg::GaplessExtension
 Chaplo::gbwt_thread_t
 CGBWTConfig
 Cvg::GBWTHandler
 Cvg::GenomeState
 ►Cvg::GenomeStateCommand
 Cvg::GenotypeDescribes a genotype at a particular locus
 Cvg::GenotypeLikelihoodCalculator
 ►Cvg::GenotypePriorCalculator
 Cvg::Genotyper
 Cvg::algorithms::GFAParser
 Cvg::GFFReader
 Cvg::GFFRecord
 CGiraffeMainOptionsOptions struct for options for the Giraffe driver (i.e. this file)
 Cvg::algorithms::Graph
 Cvg::Graph
 Cvg::DozeuInterface::graph_pos_s
 ►Cvg::GraphCaller
 CGraphHandler
 Cvg::GraphSynchronizer
 Cvg::FlowSort::Growth
 Chandlegraph::handle_tRepresents a traversal of a node in a graph in a particular direction
 ►Chandlegraph::HandleGraph
 Cvg::HandleGraphNodeSet
 Cvg::temp_file::Handler
 Cxg::temp_file::Handler
 Chaplo::haplo_DP
 Chaplo::haplo_DP_column
 Chaplo::haplo_DP_rectangle
 Cvg::PhasedGenome::Haplotype
 Cvg::PhasedGenome::HaplotypeNode
 Cvg::HaplotypePartitioner
 Cvg::Haplotypes
 CHaplotypesConfig
 Cstd::hash< const vg::Snarl >Hash function for Snarls
 Cstd::hash< handlegraph::edge_t >
 Cstd::hash< handlegraph::handle_t >
 Cstd::hash< handlegraph::net_handle_t >
 Cstd::hash< handlegraph::path_handle_t >
 Cstd::hash< handlegraph::step_handle_t >
 Cstd::hash< pair< A, B > >
 Cstd::hash< std::tuple< TT... > >
 Cstd::hash< vg::NodeSide >
 Cstd::hash< vg::NodeTraversal >Hash function for NodeTraversals
 Cvg::Genotyper::hash_ambiguous_allele_set
 Cvg::Genotyper::hash_node_traversal
 Cvg::Genotyper::hash_oriented_edge
 ►CHashGraph
 Chaplo::hDP_gbwt_graph_accessor< GBWTType >
 Cvg::Haplotypes::HeaderHeader of the serialized file
 ChFILE_backend
 Cvg::io::hFILE_cppstream
 Cvg::MEMClusterer::HitEdge
 Cvg::MEMClusterer::HitGraph
 Cvg::MEMClusterer::HitNode
 ►Cvg::HTSWriter
 Cvg::IDScanner< Message >
 Cvg::IncrementIter
 Cvg::IndexFile
 Cvg::IndexingParameters
 Cvg::IndexingPlan
 Cvg::IndexRecipe
 Cvg::IndexRegistry
 Chaplo::int_itvl_t
 ►Cistream
 Cvg::Funnel::ItemRepresents an Item whose provenance we track
 Cvg::ShuffledPairs::iterator
 Cvg::PhasedGenome::iterator
 Chandlegraph::PathForEachSocket::iterator
 Cstd::iterator_traits< vg::PhasedGenome::iterator >
 Cvg::IncrementalSubgraph::IterFCmp
 Cjob_type
 Cvg::JobSchedule
 Cjson_autoptr
 Cvg::io::JSONStreamHelper< T >
 Cvg::kff_recoding_tA mapping of character values from KFF encoding to minimizer index encoding
 Cvg::kmer_t
 Cvg::algorithms::kmer_tStores a kmer in the context of a graph
 Cvg::KmerMatchUsed to serialize kmer matches
 Cvg::KmerPosition
 Cvg::LazyRNG
 Chaplo::linear_haplo_structure
 Cvg::Recombinator::LocalHaplotypeA local haplotype sequence within a single subchain
 Cvg::LocationSupportSupport pinned to a location, which can be either a node or an edge
 Cvg::GraphSynchronizer::Lock
 Cvg::LocusDescribes a genetic locus with multiple possible alleles, a genotype, and observational support
 Cvg::Mapping
 Cvg::mapping_t
 Cvg::MappingHash
 CMappingRun
 Cvg::NGSSimulator::MarkovDistribution< From, To >
 Cvg::NGSSimulator::MarkovDistribution< pair< uint8_t, bool >, pair< pair< uint8_t, bool >, pair< uint8_t, bool > > >
 Cvg::MatchPos
 Cvg::MaximalExactMatch
 Cvg::MCMCGenotyper
 Cvg::MEMAccelerator
 Cvg::MEMChainModel
 Cvg::MEMChainModelVertex
 ►Cvg::MEMClusterer
 Cvg::IntegratedSnarlFinder::MergedAdjacencyGraph
 Cvg::io::MessageEmitter
 Cvg::io::MessageIterator
 Cvg::MinimizerMapper::Minimizer
 Cvg::MIPayload
 Cvg::MIPayloadValues
 Cvg::multipath_alignment_t
 Cvg::MultipathAlignment
 Cvg::MultipathAlignmentGraph
 Cvg::MultipathProblem
 ►Chandlegraph::NamedNodeBackTranslation
 ►Cvg::NameMapper
 Chandlegraph::net_handle_t
 Cvg::algorithms::Node
 Cvg::NodeNodes store sequence data
 Cvg::NodePileup
 Cvg::NodeSide
 Cvg::NodeTraversal
 Cvg::normal_distribution< T >
 Chandlegraph::number_bool_packingDefine a way to pack an integer and an orientation bit into a handle_t
 ►Cvg::OptionInterface
 Cvg::OptionValueParser< Value >
 Cvg::OptionValueParser< vector< Item > >
 Cvg::DozeuInterface::OrderedGraph
 ►Cvg::OrientedDistanceMeasurer
 ►Costream
 ►CPackedGraph
 Cvg::Packer
 Cvg::Funnel::PaintableSpace
 ►Cvg::PairedEndMapper
 Cvg::ParallelKFFReader
 Cvg::Recombinator::ParametersParameters for generate_haplotypes()
 Cvg::HaplotypePartitioner::ParametersParameters for partition_haplotypes()
 Cvg::Path
 Chandlegraph::path_handle_tRepresents the internal id of a path entity
 Cvg::path_mapping_t
 Cvg::path_t
 Cvg::PathBranch
 Cvg::PathChunker
 Cvg::PathComponentIndex
 Chandlegraph::PathForEachSocket
 ►CPathHandleGraphProxy
 Cvg::PathIndex
 Cvg::MatchPos::PathList
 ►Chandlegraph::PathMetadata
 Cvg::PathNode
 Cvg::Paths
 Cvg::PhasedGenome
 Cvg::PhaseUnfolder
 Cvg::Pictographs
 Cvg::PileupBundle up Node and Edge pileups
 Cvg::VG::PlanStructure for managing parallel construction of a graph
 Cvg::Position
 Cvg::position_t
 Cvg::PositionIDScanner< Message >
 Cvg::subcommand::Preset
 ►Cvg::Progressive
 Cvg::io::ProtobufEmitter< T >
 Cvg::io::ProtobufIterator< T >
 CPruningParameters
 Cvg::read_alignment_index_tType to point to an alignment of a known read
 Cvg::ReadFilter< Read >
 Cvg::ReadMasker
 Cvg::RebuildJob
 Cvg::RebuildParametersParameters for rebuild_gbwt
 Cvg::Recombinator
 Cvg::RecombinatorHaplotype
 CReferenceInterval
 Cvg::Region
 Cvg::RegionExpander
 Cvg::io::Registry
 Chandlegraph::return_type_of< Function >
 Chandlegraph::return_type_of< Returns(*)(Args...)>
 Chandlegraph::return_type_of< Returns(Owner::*)(Args...) const >
 Chandlegraph::return_type_of< Returns(Owner::*)(Args...)>
 Chaplo::haploMath::RRMemo
 ►Cruntime_error
 Cvg::WFATree::ScoreProperties
 ►Chaplo::ScoreProvider
 CScoringOptionsOptions struct for scoring-related parameters. Defaults are in aligner.hpp
 Cvg::SnarlDistanceIndexClusterer::SeedSeed information used in Giraffe
 Cvg::SnarlDistanceIndexClusterer::SeedCacheSeed information used for clustering
 Cvg::SeqComplexity< MaxOrder >
 ►Chandlegraph::Serializable
 Cvg::ShuffledPairs
 Cvg::SmallBitset
 Cvg::SnarlDescribes a subgraph that is connected to the rest of the graph by two nodes
 Cvg::NestedCachedPackedTraversalSupportFinder::snarl_less
 ►Cvg::SnarlCaller
 ►Chandlegraph::SnarlDecomposition
 Cvg::SnarlDistanceIndexClusterer
 ►Cvg::SnarlFinder
 Cvg::SnarlManager
 Cvg::SnarlManager::SnarlRecord
 Cvg::SnarlState
 Cvg::SnarlTraversal
 Cvg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
 Cvg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
 Chaplo::linear_haplo_structure::SNVvector
 ►Csparse_hash_map
 ►Csparse_hash_set
 Cvg::SpliceRegion
 Cvg::SpliceStats
 Cvg::SSWAligner
 Cvg::Funnel::StageRepresents a Stage which is a series of Items, which track their own provenance
 Cvg::state_hash
 Cvg::Recombinator::StatisticsStatistics on the generated haplotypes
 Chandlegraph::step_handle_tA step handle is an opaque reference to a single step of an oriented node on a path in a graph
 ►Cstreambuf
 ►Cvg::StreamIndexBase
 Cvg::io::StreamMultiplexer
 Cvg::HaplotypePartitioner::Subchain
 Cvg::Haplotypes::SubchainRepresentation of a subchain
 Cvg::subcommand::Subcommand
 Cvg::SubpathA non-branching path of a MultipathAlignment
 Cvg::subpath_t
 Cvg::SummaryStatistics
 Cvg::SupportAggregates information about the reads supporting an allele
 Cvg::io::Registry::Tables
 Cvg::TargetValueSearch
 Cvg::Watchdog::thread_state_t
 ►Cvg::subcommand::TickChainLink
 Cvg::Haplotypes::TopLevelChainRepresentation of a top-level chain
 Cvg::algorithms::TracedScore
 Cvg::Transcript
 Cvg::Transcriptome
 ►Cvg::TranscriptPath
 Cvg::Translation
 Cvg::Translator
 ►Cvg::TraversalFinder
 ►Cvg::TraversalSupportCalculator
 ►Cvg::TraversalSupportFinder
 Cvg::Tree< T >
 Cvg::TreeNode< T >
 Cvg::BitStringTree< Item >::TreeNode
 ►Ctrue_type
 Cvg::truncated_normal_distribution< T >
 Cvg::uniform_int_distribution< T >
 Cvg::uniform_int_distribution< size_t >
 Cvg::uniform_int_distribution< uint8_t >
 Cvg::uniform_real_distribution< T >
 Cvg::uniform_real_distribution< double >
 ►CUnionFind
 Cvg::VcfBuffer
 ►Cvg::VCFOutputCaller
 Cvg::VcfRecordConverter
 Cvg::VcfRecordFilter
 ►Cvector
 CVectorizer
 Cvg::VectorView< Item >
 Cvg::VectorViewInverse
 Cvg::VersionClass for holding vg version and build environment information
 Cvg::VGIndexes
 Cvg::VGset
 Cvg::VisitDescribes a step of a walk through a Snarl either on a node or through a child Snarl
 Cvg::Viz
 Cvg::io::VPKG
 Cvg::algorithms::walk_tRecord a <=k-length walk in the context of a graph
 Cvg::wang_hash< T, ImplementationMatched >
 Cvg::wang_hash< handle_t >
 Cvg::wang_hash< handlegraph::net_handle_t >
 Cvg::wang_hash< NodeSide >
 Cvg::wang_hash< NodeTraversal >Hash function for NodeTraversals
 Cvg::wang_hash< path_handle_t >
 Cvg::wang_hash< std::pair< A, B > >
 Cvg::wang_hash< T * >
 Cvg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >
 Cvg::Watchdog
 Cvg::FlowSort::WeightedGraph
 Cvg::WFAAlignment
 Cvg::WFAExtender
 Cvg::WFANode
 Cvg::WFAPoint
 Cvg::WFATree
 Cvg::WideningPRNG< PRNG, OutType >
 Cvg::WindowedVcfBuffer
 Cvg::WrappingPositionScanner< Message >
 Cxg::XGPath
 ►CZeroCopyInputStream
 ►CZeroCopyOutputStream
 Ccompare_gaf
 Cvg::Configurable
 Cvg::ConfigurableParser
 Cvg::ConnectionAn edge in a MultipathAlignment between Subpaths that may not be contiguous in the graph
 Cvg::connection_t
 ►Cvg::ConsistencyCalculator
 Cvg::VectorView< Item >::const_iteratorRandom access iterator
 Cvg::ConstructedChunk
 Cvg::ContractingGraph
 Cvg::count_back_inserter< T >
 Cvg::Counts
 Cvg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
 Cvg::DeletionAligner
 Cvg::DinucleotideMachine
 Cvg::discrete_distribution< T >We provide a partial discrete_distribution implementation that is just the parts we need
 ►Cvg::DistanceHeuristic
 ►Cvg::DozeuInterface
 Cvg::MEMClusterer::DPScoreComparator
 Cvg::algorithms::Edge
 Cvg::Edge
 Cvg::EdgePileupKeep pileup-like record for reads that span edges
 Cvg::Edit
 Cvg::edit_t
 Cvg::endianness< IntType >
 Cvg::WFAExtender::ErrorModel
 Cvg::WFAExtender::ErrorModel::Event
 ►Cexception
 Cvg::Exon
 ►Cvg::Explainer
 ►Cfalse_type
 Cvg::IncrementalSubgraph::FCmp
 Cvg::FeatureSet::Feature
 Cvg::FeatureSet
 Cvg::Filter
 Cvg::Funnel::FilterPerformance
 Cvg::FlowSort
 Cvg::FragmentLengthDistribution
 Cvg::FragmentLengthStatistics
 Cvg::Funnel
 CGafFile
 ►Cvg::GAFOutputCaller
 Cgafkluge::GafRecord
 Cgafkluge::GafStep
 Cvg::GaplessExtender
 Cvg::GaplessExtension
 Chaplo::gbwt_thread_t
 CGBWTConfig
 Cvg::GBWTHandler
 Cvg::GenomeState
 ►Cvg::GenomeStateCommand
 Cvg::GenotypeDescribes a genotype at a particular locus
 Cvg::GenotypeLikelihoodCalculator
 ►Cvg::GenotypePriorCalculator
 Cvg::Genotyper
 Cvg::algorithms::GFAParser
 Cvg::GFFReader
 Cvg::GFFRecord
 CGiraffeMainOptionsOptions struct for options for the Giraffe driver (i.e. this file)
 Cvg::algorithms::Graph
 Cvg::Graph
 Cvg::DozeuInterface::graph_pos_s
 ►Cvg::GraphCaller
 CGraphHandler
 Cvg::GraphSynchronizer
 Cgreater_gaffile
 Cvg::FlowSort::Growth
 Chandlegraph::handle_tRepresents a traversal of a node in a graph in a particular direction
 ►Chandlegraph::HandleGraph
 Cvg::HandleGraphNodeSet
 Cvg::temp_file::Handler
 Cxg::temp_file::Handler
 Chaplo::haplo_DP
 Chaplo::haplo_DP_column
 Chaplo::haplo_DP_rectangle
 Cvg::PhasedGenome::Haplotype
 Cvg::PhasedGenome::HaplotypeNode
 Cvg::HaplotypePartitioner
 Cvg::Haplotypes
 CHaplotypesConfig
 Cstd::hash< const vg::Snarl >Hash function for Snarls
 Cstd::hash< handlegraph::edge_t >
 Cstd::hash< handlegraph::handle_t >
 Cstd::hash< handlegraph::net_handle_t >
 Cstd::hash< handlegraph::path_handle_t >
 Cstd::hash< handlegraph::step_handle_t >
 Cstd::hash< pair< A, B > >
 Cstd::hash< std::tuple< TT... > >
 Cstd::hash< vg::NodeSide >
 Cstd::hash< vg::NodeTraversal >Hash function for NodeTraversals
 Cvg::Genotyper::hash_ambiguous_allele_set
 Cvg::Genotyper::hash_node_traversal
 Cvg::Genotyper::hash_oriented_edge
 ►CHashGraph
 Chaplo::hDP_gbwt_graph_accessor< GBWTType >
 Cvg::Haplotypes::HeaderHeader of the serialized file
 ChFILE_backend
 Cvg::io::hFILE_cppstream
 Cvg::MEMClusterer::HitEdge
 Cvg::MEMClusterer::HitGraph
 Cvg::MEMClusterer::HitNode
 ►Cvg::HTSWriter
 Cvg::IDScanner< Message >
 Cvg::IncrementIter
 Cvg::IndexFile
 Cvg::IndexingParameters
 Cvg::IndexingPlan
 Cvg::IndexRecipe
 Cvg::IndexRegistry
 Chaplo::int_itvl_t
 ►Cistream
 Cvg::Funnel::ItemRepresents an Item whose provenance we track
 Cvg::ShuffledPairs::iterator
 Chandlegraph::PathForEachSocket::iterator
 Cvg::PhasedGenome::iterator
 Cstd::iterator_traits< vg::PhasedGenome::iterator >
 Cvg::IncrementalSubgraph::IterFCmp
 Cjob_type
 Cvg::JobSchedule
 Cjson_autoptr
 Cvg::io::JSONStreamHelper< T >
 Cvg::kff_recoding_tA mapping of character values from KFF encoding to minimizer index encoding
 Cvg::kmer_t
 Cvg::algorithms::kmer_tStores a kmer in the context of a graph
 Cvg::KmerMatchUsed to serialize kmer matches
 Cvg::KmerPosition
 Cvg::LazyRNG
 Chaplo::linear_haplo_structure
 Cvg::Recombinator::LocalHaplotypeA local haplotype sequence within a single subchain
 Cvg::LocationSupportSupport pinned to a location, which can be either a node or an edge
 Cvg::GraphSynchronizer::Lock
 Cvg::LocusDescribes a genetic locus with multiple possible alleles, a genotype, and observational support
 Cvg::Mapping
 Cvg::mapping_t
 Cvg::MappingHash
 CMappingRun
 Cvg::NGSSimulator::MarkovDistribution< From, To >
 Cvg::NGSSimulator::MarkovDistribution< pair< uint8_t, bool >, pair< pair< uint8_t, bool >, pair< uint8_t, bool > > >
 Cvg::MatchPos
 Cvg::MaximalExactMatch
 Cvg::MCMCGenotyper
 Cvg::MEMAccelerator
 Cvg::MEMChainModel
 Cvg::MEMChainModelVertex
 ►Cvg::MEMClusterer
 Cvg::IntegratedSnarlFinder::MergedAdjacencyGraph
 Cvg::io::MessageEmitter
 Cvg::io::MessageIterator
 Cvg::MinimizerMapper::Minimizer
 Cvg::MIPayload
 Cvg::MIPayloadValues
 Cvg::multipath_alignment_t
 Cvg::MultipathAlignment
 Cvg::MultipathAlignmentGraph
 Cvg::MultipathProblem
 ►Chandlegraph::NamedNodeBackTranslation
 ►Cvg::NameMapper
 Chandlegraph::net_handle_t
 Cvg::algorithms::Node
 Cvg::NodeNodes store sequence data
 Cvg::NodePileup
 Cvg::NodeSide
 Cvg::NodeTraversal
 Cvg::normal_distribution< T >
 Chandlegraph::number_bool_packingDefine a way to pack an integer and an orientation bit into a handle_t
 ►Cvg::OptionInterface
 Cvg::OptionValueParser< Value >
 Cvg::OptionValueParser< vector< Item > >
 Cvg::DozeuInterface::OrderedGraph
 ►Cvg::OrientedDistanceMeasurer
 ►Costream
 ►CPackedGraph
 Cvg::Packer
 Cvg::Funnel::PaintableSpace
 ►Cvg::PairedEndMapper
 Cvg::ParallelKFFReader
 Cvg::HaplotypePartitioner::ParametersParameters for partition_haplotypes()
 Cvg::Recombinator::ParametersParameters for generate_haplotypes()
 Cvg::Path
 Chandlegraph::path_handle_tRepresents the internal id of a path entity
 Cvg::path_mapping_t
 Cvg::path_t
 Cvg::PathBranch
 Cvg::PathChunker
 Cvg::PathComponentIndex
 Chandlegraph::PathForEachSocket
 ►CPathHandleGraphProxy
 Cvg::PathIndex
 Cvg::MatchPos::PathList
 ►Chandlegraph::PathMetadata
 Cvg::PathNode
 Cvg::Paths
 Cvg::PhasedGenome
 Cvg::PhaseUnfolder
 Cvg::Pictographs
 Cvg::PileupBundle up Node and Edge pileups
 Cvg::VG::PlanStructure for managing parallel construction of a graph
 Cvg::Position
 Cvg::position_t
 Cvg::PositionIDScanner< Message >
 Cvg::subcommand::Preset
 ►Cvg::Progressive
 Cvg::io::ProtobufEmitter< T >
 Cvg::io::ProtobufIterator< T >
 CPruningParameters
 Cvg::read_alignment_index_tType to point to an alignment of a known read
 Cvg::ReadFilter< Read >
 Cvg::ReadMasker
 Cvg::RebuildJob
 Cvg::RebuildParametersParameters for rebuild_gbwt
 Cvg::Recombinator
 Cvg::RecombinatorHaplotype
 CReferenceInterval
 Cvg::Region
 Cvg::RegionExpander
 Cvg::io::Registry
 Chandlegraph::return_type_of< Function >
 Chandlegraph::return_type_of< Returns(*)(Args...)>
 Chandlegraph::return_type_of< Returns(Owner::*)(Args...) const >
 Chandlegraph::return_type_of< Returns(Owner::*)(Args...)>
 Chaplo::haploMath::RRMemo
 ►Cruntime_error
 Cvg::WFATree::ScoreProperties
 ►Chaplo::ScoreProvider
 CScoringOptionsOptions struct for scoring-related parameters. Defaults are in aligner.hpp
 Cvg::SnarlDistanceIndexClusterer::SeedSeed information used in Giraffe
 Cvg::SnarlDistanceIndexClusterer::SeedCacheSeed information used for clustering
 Cvg::SeqComplexity< MaxOrder >
 ►Chandlegraph::Serializable
 Cvg::ShuffledPairs
 Cvg::SmallBitset
 Cvg::SnarlDescribes a subgraph that is connected to the rest of the graph by two nodes
 Cvg::NestedCachedPackedTraversalSupportFinder::snarl_less
 ►Cvg::SnarlCaller
 ►Chandlegraph::SnarlDecomposition
 Cvg::SnarlDistanceIndexClusterer
 ►Cvg::SnarlFinder
 Cvg::SnarlManager
 Cvg::SnarlManager::SnarlRecord
 Cvg::SnarlState
 Cvg::SnarlTraversal
 Cvg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
 Cvg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
 Chaplo::linear_haplo_structure::SNVvector
 ►Csparse_hash_map
 ►Csparse_hash_set
 Cvg::SpliceRegion
 Cvg::SpliceStats
 Cvg::SSWAligner
 Cvg::Funnel::StageRepresents a Stage which is a series of Items, which track their own provenance
 Cvg::state_hash
 Cvg::Recombinator::StatisticsStatistics on the generated haplotypes
 Chandlegraph::step_handle_tA step handle is an opaque reference to a single step of an oriented node on a path in a graph
 ►Cstreambuf
 ►Cvg::StreamIndexBase
 Cvg::io::StreamMultiplexer
 Cvg::Haplotypes::SubchainRepresentation of a subchain
 Cvg::HaplotypePartitioner::Subchain
 Cvg::subcommand::Subcommand
 Cvg::SubpathA non-branching path of a MultipathAlignment
 Cvg::subpath_t
 Cvg::SummaryStatistics
 Cvg::SupportAggregates information about the reads supporting an allele
 Cvg::io::Registry::Tables
 Cvg::TargetValueSearch
 Cvg::Watchdog::thread_state_t
 ►Cvg::subcommand::TickChainLink
 Cvg::Haplotypes::TopLevelChainRepresentation of a top-level chain
 Cvg::algorithms::TracedScore
 Cvg::Transcript
 Cvg::Transcriptome
 ►Cvg::TranscriptPath
 Cvg::Translation
 Cvg::Translator
 ►Cvg::TraversalFinder
 ►Cvg::TraversalSupportCalculator
 ►Cvg::TraversalSupportFinder
 Cvg::Tree< T >
 Cvg::BitStringTree< Item >::TreeNode
 Cvg::TreeNode< T >
 ►Ctrue_type
 Cvg::truncated_normal_distribution< T >
 Cvg::uniform_int_distribution< T >
 Cvg::uniform_int_distribution< size_t >
 Cvg::uniform_int_distribution< uint8_t >
 Cvg::uniform_real_distribution< T >
 Cvg::uniform_real_distribution< double >
 ►CUnionFind
 Cvg::VcfBuffer
 ►Cvg::VCFOutputCaller
 Cvg::VcfRecordConverter
 Cvg::VcfRecordFilter
 ►Cvector
 CVectorizer
 Cvg::VectorView< Item >
 Cvg::VectorViewInverse
 Cvg::VersionClass for holding vg version and build environment information
 Cvg::VGIndexes
 Cvg::VGset
 Cvg::VisitDescribes a step of a walk through a Snarl either on a node or through a child Snarl
 Cvg::Viz
 Cvg::io::VPKG
 Cvg::algorithms::walk_tRecord a <=k-length walk in the context of a graph
 Cvg::wang_hash< T, ImplementationMatched >
 Cvg::wang_hash< handle_t >
 Cvg::wang_hash< handlegraph::net_handle_t >
 Cvg::wang_hash< NodeSide >
 Cvg::wang_hash< NodeTraversal >Hash function for NodeTraversals
 Cvg::wang_hash< path_handle_t >
 Cvg::wang_hash< std::pair< A, B > >
 Cvg::wang_hash< T * >
 Cvg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >
 Cvg::Watchdog
 Cvg::FlowSort::WeightedGraph
 Cvg::WFAAlignment
 Cvg::WFAExtender
 Cvg::WFANode
 Cvg::WFAPoint
 Cvg::WFATree
 Cvg::WideningPRNG< PRNG, OutType >
 Cvg::WindowedVcfBuffer
 Cvg::WrappingPositionScanner< Message >
 Cxg::XGPath
 ►CZeroCopyInputStream
 ►CZeroCopyOutputStream
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vg +
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tools for working with variation graphs
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+ +
+ +
+
+
+
GafFile Member List
+
+
+ +

This is the complete list of members for GafFile, including all inherited members.

+ + + +
file_iGafFile
gafGafFile
+ + +
+Generated by   +doxygen + 1.8.17 +
+ + diff --git a/structGafFile.html b/structGafFile.html new file mode 100644 index 00000000000..e6198c52a2a --- /dev/null +++ b/structGafFile.html @@ -0,0 +1,121 @@ + + + + + + + +vg: GafFile Struct Reference + + + + + + + + + +
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tools for working with variation graphs
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+Public Attributes | +List of all members
+
+
GafFile Struct Reference
+
+
+ + + + + + +

+Public Attributes

gafkluge::GafRecord gaf
 
int file_i
 
+

Member Data Documentation

+ +

◆ file_i

+ +
+
+ + + + +
int GafFile::file_i
+
+ +
+
+ +

◆ gaf

+ +
+
+ + + + +
gafkluge::GafRecord GafFile::gaf
+
+ +
+
+
The documentation for this struct was generated from the following file: +
+ + +
+Generated by   +doxygen + 1.8.17 +
+ + diff --git a/structcompare__gaf-members.html b/structcompare__gaf-members.html new file mode 100644 index 00000000000..0fbb797e5d2 --- /dev/null +++ b/structcompare__gaf-members.html @@ -0,0 +1,82 @@ + + + + + + + +vg: Member List + + + + + + + + + +
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compare_gaf Member List
+
+
+ +

This is the complete list of members for compare_gaf, including all inherited members.

+ + +
operator()(const gafkluge::GafRecord &gaf1, const gafkluge::GafRecord &gaf2)compare_gafinline
+ + +
+Generated by   +doxygen + 1.8.17 +
+ + diff --git a/structcompare__gaf.html b/structcompare__gaf.html new file mode 100644 index 00000000000..ff80bf2ffe7 --- /dev/null +++ b/structcompare__gaf.html @@ -0,0 +1,127 @@ + + + + + + + +vg: compare_gaf Struct Reference + + + + + + + + + +
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tools for working with variation graphs
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+Public Member Functions | +List of all members
+
+
compare_gaf Struct Reference
+
+
+ + + + +

+Public Member Functions

bool operator() (const gafkluge::GafRecord &gaf1, const gafkluge::GafRecord &gaf2)
 
+

Member Function Documentation

+ +

◆ operator()()

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
bool compare_gaf::operator() (const gafkluge::GafRecord & gaf1,
const gafkluge::GafRecord & gaf2 
)
+ 		+inline
+
+ +
+
+
The documentation for this struct was generated from the following file: +
+ + +
+Generated by   +doxygen + 1.8.17 +
+ + diff --git a/structgreater__gaffile-members.html b/structgreater__gaffile-members.html new file mode 100644 index 00000000000..293bd35b1ca --- /dev/null +++ b/structgreater__gaffile-members.html @@ -0,0 +1,82 @@ + + + + + + + +vg: Member List + + + + + + + + + +
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+
+
greater_gaffile Member List
+
+
+ +

This is the complete list of members for greater_gaffile, including all inherited members.

+ + +
operator()(const GafFile &gf1, const GafFile &gf2)greater_gaffileinline
+ + +
+Generated by   +doxygen + 1.8.17 +
+ + diff --git a/structgreater__gaffile.html b/structgreater__gaffile.html new file mode 100644 index 00000000000..eadb17af7b9 --- /dev/null +++ b/structgreater__gaffile.html @@ -0,0 +1,127 @@ + + + + + + + +vg: greater_gaffile Struct Reference + + + + + + + + + +
+
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+Public Member Functions | +List of all members
+
+
greater_gaffile Struct Reference
+
+
+ + + + +

+Public Member Functions

bool operator() (const GafFile &gf1, const GafFile &gf2)
 
+

Member Function Documentation

+ +

◆ operator()()

+ +
+
+ + + + + +
+ + + + + + + + + + + + + + + + + + +
bool greater_gaffile::operator() (const GafFile & gf1,
const GafFile & gf2 
)
+ 		+inline
+
+ +
+
+
The documentation for this struct was generated from the following file: +
+ + +
+Generated by   +doxygen + 1.8.17 +
+ +