nvbio::bowtie2::cuda::ParamsPOD Struct Reference

Detailed description

A POD structure holding all of nvBowtie's parameters

Definition at line 95 of file params.h.

#include <params.h>

Inheritance diagram for nvbio::bowtie2::cuda::ParamsPOD:

Public Members
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

uint32 nvbio::bowtie2::cuda::ParamsPOD::alignment_type

Definition at line 103 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::allow_sub

Definition at line 115 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::avg_read_length

Definition at line 120 of file params.h.

DebugState nvbio::bowtie2::cuda::ParamsPOD::debug

Definition at line 137 of file params.h.

bool nvbio::bowtie2::cuda::ParamsPOD::fw

Definition at line 99 of file params.h.

bool nvbio::bowtie2::cuda::ParamsPOD::keep_stats

Definition at line 97 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::mapq_filter

Definition at line 117 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::max_batch_size

Definition at line 119 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::max_dist

Definition at line 108 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::max_effort

Definition at line 110 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::max_effort_init

Definition at line 109 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::max_ext

Definition at line 112 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::max_frag_len

Definition at line 130 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::max_hits

Definition at line 107 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::max_reseed

Definition at line 113 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::min_ext

Definition at line 111 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::min_frag_len

Definition at line 129 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::min_read_len

Definition at line 118 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::mode

Definition at line 101 of file params.h.

bool nvbio::bowtie2::cuda::ParamsPOD::pe_discordant

Definition at line 128 of file params.h.

bool nvbio::bowtie2::cuda::ParamsPOD::pe_dovetail

Definition at line 126 of file params.h.

bool nvbio::bowtie2::cuda::ParamsPOD::pe_overlap

Definition at line 125 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::pe_policy

Definition at line 124 of file params.h.

bool nvbio::bowtie2::cuda::ParamsPOD::pe_unpaired

Definition at line 127 of file params.h.

bool nvbio::bowtie2::cuda::ParamsPOD::randomized

Definition at line 98 of file params.h.

bool nvbio::bowtie2::cuda::ParamsPOD::rc

Definition at line 100 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::rep_seeds

Definition at line 114 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::scoring_mode

Definition at line 102 of file params.h.

UberScoringScheme nvbio::bowtie2::cuda::ParamsPOD::scoring_scheme

Definition at line 133 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::scoring_window

Definition at line 136 of file params.h.

SimpleFunc nvbio::bowtie2::cuda::ParamsPOD::seed_freq

Definition at line 106 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::seed_len

Definition at line 105 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::subseed_len

Definition at line 116 of file params.h.

uint32 nvbio::bowtie2::cuda::ParamsPOD::top_seed

Definition at line 104 of file params.h.

bool nvbio::bowtie2::cuda::ParamsPOD::ungapped_mates

Definition at line 121 of file params.h.

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

• E:/git/nvbio/nvBowtie/bowtie2/cuda/params.h