haplo Namespace Reference

Namespaces
	haploMath

Classes
struct	gbwt_thread_t
class	GBWTScoreProvider
	Score haplotypes using a GBWT haplotype database (normal or dynamic) More...
struct	haplo_DP
struct	haplo_DP_column
struct	haplo_DP_rectangle
class	hDP_gbwt_graph_accessor
struct	int_itvl_t
struct	linear_haplo_structure
class	LinearScoreProvider
	Score haplotypes using a linear_haplo_structure. More...
class	ScoreProvider

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

Functions
gbwt_thread_t	path_to_gbwt_thread_t (const vg::Path &path)

Variables
bool	warn_on_score_fail = false

Typedef Documentation

haplo_score_type

typedef pair<double, bool> haplo::haplo_score_type

IncrementalSearchState

using haplo::IncrementalSearchState = typedef gbwt::SearchState

Incremental haplotype search range type used for ScoreProvider's incremental search API. Default constructed, represents an empty or un-started search. Supports an empty() and a length(). Copyable. TODO: There's some overlap with the graph accessors here, but I don't understand them enough to work out exactly what it is and eliminate it. TODO: This should become a real type (base class and implementations wrapping implementation-specific data) when we get any other implementations.

Function Documentation

path_to_gbwt_thread_t()

gbwt_thread_t haplo::path_to_gbwt_thread_t

(

const vg::Path &

path

)

Variable Documentation

warn_on_score_fail

bool haplo::warn_on_score_fail = false