All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Public Members | List of all members
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.

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