haplo::linear_haplo_structure Struct Reference

#include <haplotypes.hpp>

Classes
class	linearUnrepresentable
struct	SNVvector

Public Types
enum	nodeType { ref_span, snv, invalid }
typedef enum haplo::linear_haplo_structure::nodeType	nodeType

Public Member Functions
	linear_haplo_structure (istream &slls_index, double log_mut_penalty, double log_recomb_penalty, const vg::PathPositionHandleGraph &graph, vg::path_handle_t ref_path_handle)
	~linear_haplo_structure ()
haplo_score_type	score (const vg::Path &path) const
inputHaplotype *	path_to_input_haplotype (const vg::Path &path) const
size_t	position_assuming_acyclic (int64_t node_id) const
nodeType	get_type (int64_t node_id) const
int64_t	path_mapping_node_id (const vg::Path &path, size_t i) const
size_t	path_mapping_offset (const vg::Path &path, size_t i) const
int64_t	get_SNP_ref_position (size_t node_id) const
SNVvector	SNVs (const vg::Path &path) const
bool	is_snv (int64_t node_id) const
bool	is_solitary_ref (int64_t node_id) const
bool	sn_deletion_between_ref (int64_t left, int64_t right) const
int64_t	get_ref_following (int64_t node_id) const
alleleValue	get_SNV_allele (int64_t node_id) const

Private Attributes
siteIndex *	index = nullptr
haplotypeCohort *	cohort = nullptr
penaltySet *	penalties = nullptr
const vg::PathPositionHandleGraph &	graph
vg::path_handle_t	ref_path_handle

Member Typedef Documentation

nodeType

typedef enum haplo::linear_haplo_structure::nodeType haplo::linear_haplo_structure::nodeType

Member Enumeration Documentation

nodeType

enum haplo::linear_haplo_structure::nodeType

Enumerator
ref_span
snv
invalid

Constructor & Destructor Documentation

linear_haplo_structure()

haplo::linear_haplo_structure::linear_haplo_structure	(	istream &	slls_index,
		double	log_mut_penalty,
		double	log_recomb_penalty,
		const vg::PathPositionHandleGraph &	graph,
		vg::path_handle_t	ref_path_handle
	)

Make a new linear_haplo_structure with the given indexes, mutation and recombination scoring parameters, and reference path in the graph. Penalties must be negative, and ought to be something like -9*2.3 mutation and -6*2.3 recombination.

~linear_haplo_structure()

haplo::linear_haplo_structure::~linear_haplo_structure

(

)

Member Function Documentation

get_ref_following()

int64_t haplo::linear_haplo_structure::get_ref_following

(

int64_t

node_id

)

const

get_SNP_ref_position()

int64_t haplo::linear_haplo_structure::get_SNP_ref_position

(

size_t

node_id

)

const

get_SNV_allele()

alleleValue haplo::linear_haplo_structure::get_SNV_allele

(

int64_t

node_id

)

const

get_type()

linear_haplo_structure::nodeType haplo::linear_haplo_structure::get_type

(

int64_t

node_id

)

const

is_snv()

bool haplo::linear_haplo_structure::is_snv

(

int64_t

node_id

)

const

is_solitary_ref()

bool haplo::linear_haplo_structure::is_solitary_ref

(

int64_t

node_id

)

const

path_mapping_node_id()

int64_t haplo::linear_haplo_structure::path_mapping_node_id	(	const vg::Path &	path,
		size_t	i
	)		const

path_mapping_offset()

size_t haplo::linear_haplo_structure::path_mapping_offset	(	const vg::Path &	path,
		size_t	i
	)		const

path_to_input_haplotype()

inputHaplotype * haplo::linear_haplo_structure::path_to_input_haplotype

(

const vg::Path &

path

)

const

position_assuming_acyclic()

size_t haplo::linear_haplo_structure::position_assuming_acyclic

(

int64_t

node_id

)

const

score()

haplo_score_type haplo::linear_haplo_structure::score

(

const vg::Path &

path

)

const

sn_deletion_between_ref()

bool haplo::linear_haplo_structure::sn_deletion_between_ref	(	int64_t	left,
		int64_t	right
	)		const

SNVs()

linear_haplo_structure::SNVvector haplo::linear_haplo_structure::SNVs

(

const vg::Path &

path

)

const

Member Data Documentation

cohort

haplotypeCohort* haplo::linear_haplo_structure::cohort = nullptr

private

graph

const vg::PathPositionHandleGraph& haplo::linear_haplo_structure::graph

private

index

siteIndex* haplo::linear_haplo_structure::index = nullptr

private

penalties

penaltySet* haplo::linear_haplo_structure::penalties = nullptr

private

ref_path_handle

vg::path_handle_t haplo::linear_haplo_structure::ref_path_handle

private

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The documentation for this struct was generated from the following files:

• src/haplotypes.hpp
• src/haplotypes.cpp