haplotypes.hpp File Reference

#include <cmath>
#include <vector>
#include <iostream>
#include <unordered_set>
#include <vg/vg.pb.h>
#include "handle.hpp"
#include <gbwt/gbwt.h>
#include <gbwt/dynamic_gbwt.h>
#include <sublinearLS/reference.hpp>
#include <sublinearLS/penalty_set.hpp>
#include <sublinearLS/input_haplotype.hpp>
#include <sublinearLS/probability.hpp>

Classes
struct	haplo::haploMath::RRMemo
struct	haplo::int_itvl_t
struct	haplo::gbwt_thread_t
class	haplo::hDP_gbwt_graph_accessor< GBWTType >
struct	haplo::haplo_DP_rectangle
struct	haplo::haplo_DP_column
struct	haplo::haplo_DP
struct	haplo::linear_haplo_structure
class	haplo::linear_haplo_structure::linearUnrepresentable
struct	haplo::linear_haplo_structure::SNVvector
class	haplo::ScoreProvider
class	haplo::GBWTScoreProvider< GBWTType >
	Score haplotypes using a GBWT haplotype database (normal or dynamic) More...
class	haplo::LinearScoreProvider
	Score haplotypes using a linear_haplo_structure. More...

Namespaces
	haplo
	haplo::haploMath

Typedefs
typedef pair< double, bool >	haplo::haplo_score_type
using	haplo::IncrementalSearchState = gbwt::SearchState

Functions
double	haplo::haploMath::logsum (double a, double b)
double	haplo::haploMath::logdiff (double a, double b)
double	haplo::haploMath::int_weighted_sum (vector< double > values, vector< int64_t > counts)
double	haplo::haploMath::int_weighted_sum (double *values, int64_t *counts, size_t n_values)
gbwt_thread_t	haplo::path_to_gbwt_thread_t (const vg::Path &path)