nvBowtie

Detailed Description

see Architecture

Modules
	Locate
	Mapping
	Pipeline States
	Scoring
	Scoring Queues
	Select
	Alignment Module
	Defs
	Reduce
	SeedHits
	Traceback

Classes
struct	nvbio::bowtie2::cuda::packed_read
struct	nvbio::bowtie2::cuda::packed_seed
struct	nvbio::bowtie2::cuda::pack_read
struct	nvbio::bowtie2::cuda::SimpleFunc
struct	nvbio::bowtie2::cuda::ParamsPOD
struct	nvbio::bowtie2::cuda::Params

Enumerations
enum	nvbio::bowtie2::cuda::MappingMode { nvbio::bowtie2::cuda::BestMappingApprox = 0, nvbio::bowtie2::cuda::BestMappingExact = 1, nvbio::bowtie2::cuda::AllMapping = 2 }
enum	nvbio::bowtie2::cuda::ScoringMode { nvbio::bowtie2::cuda::EditDistanceMode = 0, nvbio::bowtie2::cuda::SmithWatermanMode = 1 }

Functions
const char *	nvbio::bowtie2::cuda::mapping_mode (const uint32 mode)
uint32	nvbio::bowtie2::cuda::mapping_mode (const char *str)
const char *	nvbio::bowtie2::cuda::scoring_mode (const uint32 mode)
uint32	nvbio::bowtie2::cuda::scoring_mode (const char *str)
std::map< std::string, std::string >	nvbio::bowtie2::cuda::load_options (const char *name)
void	nvbio::bowtie2::cuda::parse_options (Params &params, const std::map< std::string, std::string > &options, bool init)

Enumeration Type Documentation

enum nvbio::bowtie2::cuda::MappingMode

Enumerator
BestMappingApprox
BestMappingExact
AllMapping

Definition at line 42 of file params.h.

enum nvbio::bowtie2::cuda::ScoringMode

Enumerator
EditDistanceMode
SmithWatermanMode

Definition at line 48 of file params.h.

Function Documentation

std::map< std::string, std::string > nvbio::bowtie2::cuda::load_options

(

const char *

name)

load options from a file

Definition at line 13 of file params.cpp.

const char* nvbio::bowtie2::cuda::mapping_mode ( const uint32  mode)

inline

Definition at line 58 of file params.h.

uint32 nvbio::bowtie2::cuda::mapping_mode ( const char *  str)

inline

Definition at line 63 of file params.h.

void nvbio::bowtie2::cuda::parse_options	(	Params &	params,
		const std::map< std::string, std::string > &	options,
		bool	init
	)

parse options

Definition at line 111 of file params.cpp.

const char* nvbio::bowtie2::cuda::scoring_mode ( const uint32  mode)

inline

Definition at line 77 of file params.h.

uint32 nvbio::bowtie2::cuda::scoring_mode ( const char *  str)

inline

Definition at line 82 of file params.h.