haplo::GBWTScoreProvider< GBWTType > Class Template Reference

Score haplotypes using a GBWT haplotype database (normal or dynamic) More...

#include <haplotypes.hpp>

Inheritance diagram for haplo::GBWTScoreProvider< GBWTType >:

Public Member Functions
	GBWTScoreProvider (GBWTType &index)
pair< double, bool >	score (const vg::Path &, haploMath::RRMemo &memo)
	Score the given path usign the given memo. More...
int64_t	get_haplotype_count () const
bool	has_incremental_search () const
IncrementalSearchState	incremental_find (const vg::Position &pos) const
IncrementalSearchState	incremental_extend (const IncrementalSearchState &state, const vg::Position &pos) const
Public Member Functions inherited from haplo::ScoreProvider
virtual	~ScoreProvider ()=default

Private Attributes
GBWTType &	index

Detailed Description

template<class GBWTType>
class haplo::GBWTScoreProvider< GBWTType >

Score haplotypes using a GBWT haplotype database (normal or dynamic)

Constructor & Destructor Documentation

GBWTScoreProvider()

template<class GBWTType >

haplo::GBWTScoreProvider< GBWTType >::GBWTScoreProvider

(

GBWTType &

index

)

Member Function Documentation

get_haplotype_count()

template<class GBWTType >

int64_t haplo::GBWTScoreProvider< GBWTType >::get_haplotype_count

virtual

Return the haplotype count (number of expected haplotypes that agree with a path that is fixed in the population) that should be used to construct the memo to pass to score, or -1 if the indexes backing the ScoreProvider do not make this information available.

Reimplemented from haplo::ScoreProvider.

has_incremental_search()

template<class GBWTType >

bool haplo::GBWTScoreProvider< GBWTType >::has_incremental_search

virtual

Return true if this ScoreProvider supports incremental search for counting haplotypes.

Reimplemented from haplo::ScoreProvider.

incremental_extend()

template<class GBWTType >

IncrementalSearchState haplo::GBWTScoreProvider< GBWTType >::incremental_extend ( const IncrementalSearchState &  state, const vg::Position &  pos  ) const

virtual

Extend the given search state with the node visit described by the given Position, if incremental search is supported.

Reimplemented from haplo::ScoreProvider.

incremental_find()

template<class GBWTType >

IncrementalSearchState haplo::GBWTScoreProvider< GBWTType >::incremental_find ( const vg::Position &  pos ) const

virtual

Start a new search state with the node visit described by the given Position, if incremental search is supported.

Reimplemented from haplo::ScoreProvider.

score()

template<class GBWTType >

pair< double, bool > haplo::GBWTScoreProvider< GBWTType >::score ( const vg::Path &  , haploMath::RRMemo &  memo  )

virtual

Score the given path usign the given memo.

Implements haplo::ScoreProvider.

Member Data Documentation

index

template<class GBWTType >

GBWTType& haplo::GBWTScoreProvider< GBWTType >::index

private

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The documentation for this class was generated from the following file:

• src/haplotypes.hpp