Detailed description

A non-POD structure holding all of nvBowtie's parameters plus a few extra string options

Definition at line 143 of file params.h.

#include <params.h>

Inheritance diagram for nvbio::bowtie2::cuda::Params:

Public Members
std::string	report

std::string	scoring_file

int32	persist_batch

int32	persist_seeding

int32	persist_extension

std::string	persist_file

int32	no_multi_hits

Public Members inherited from nvbio::bowtie2::cuda::ParamsPOD
bool	keep_stats

bool	randomized

bool	fw

bool	rc

uint32	mode

uint32	scoring_mode

uint32	alignment_type

uint32	top_seed

uint32	seed_len

SimpleFunc	seed_freq

uint32	max_hits

uint32	max_dist

uint32	max_effort_init

uint32	max_effort

uint32	min_ext

uint32	max_ext

uint32	max_reseed

uint32	rep_seeds

uint32	allow_sub

uint32	subseed_len

uint32	mapq_filter

uint32	min_read_len

uint32	max_batch_size

uint32	avg_read_length

bool	ungapped_mates

uint32	pe_policy

bool	pe_overlap

bool	pe_dovetail

bool	pe_unpaired

bool	pe_discordant

uint32	min_frag_len

uint32	max_frag_len

UberScoringScheme	scoring_scheme

uint32	scoring_window

DebugState	debug

Member Data Documentation

int32 nvbio::bowtie2::cuda::Params::no_multi_hits

Definition at line 153 of file params.h.

int32 nvbio::bowtie2::cuda::Params::persist_batch

Definition at line 148 of file params.h.

int32 nvbio::bowtie2::cuda::Params::persist_extension

Definition at line 150 of file params.h.

std::string nvbio::bowtie2::cuda::Params::persist_file

Definition at line 151 of file params.h.

int32 nvbio::bowtie2::cuda::Params::persist_seeding

Definition at line 149 of file params.h.

std::string nvbio::bowtie2::cuda::Params::report

Definition at line 145 of file params.h.

std::string nvbio::bowtie2::cuda::Params::scoring_file

Definition at line 146 of file params.h.

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