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nvbio::bowtie2::cuda::Params Struct Reference

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: