FastqPuri
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_iparam_trimFilter Struct Reference

trimFilter input parameters More...

#include <struct_trimFilter.h>

Collaboration diagram for _iparam_trimFilter:
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Public Attributes

char * Ifq
 
char * Ifq2
 
char * Ifa
 
char * Iidx
 
char * Iinfo
 
char * Oprefix
 
bool uncompress
 
Adapter ad
 
Bfkmerptr_bfkmer
 
int trimQ
 
int trimN
 
int method
 
bool is_fa
 
bool is_idx
 
bool is_adapter
 
double score
 
int minQ
 
int L
 
int minL
 
int nlowQ
 
int kmersize
 
int globleft
 
int globright
 
int percent
 

Detailed Description

trimFilter input parameters

Member Data Documentation

◆ ad

Adapter _iparam_trimFilter::ad

AdapterDS trimming parameters

◆ globleft

int _iparam_trimFilter::globleft

number of bases globally trimming from the left

◆ globright

int _iparam_trimFilter::globright

number of bases globally trimming from the right

◆ Ifa

char* _iparam_trimFilter::Ifa

Input fa file (containing contamination sequences)

◆ Ifq

char* _iparam_trimFilter::Ifq

Input fq file single stranded

◆ Ifq2

char* _iparam_trimFilter::Ifq2

Input fq file read 2

◆ Iidx

char* _iparam_trimFilter::Iidx

Input index file (from an input.fa cont file)

◆ Iinfo

char* _iparam_trimFilter::Iinfo

Input index info file

◆ is_adapter

bool _iparam_trimFilter::is_adapter

true if filtering adapter sequences

◆ is_fa

bool _iparam_trimFilter::is_fa

true if a fasta file was passed as a parameter

◆ is_idx

bool _iparam_trimFilter::is_idx

true if an index file was passed as a parameter

◆ kmersize

int _iparam_trimFilter::kmersize

kmersize to look for contamination

◆ L

int _iparam_trimFilter::L

read length

◆ method

int _iparam_trimFilter::method

TREE(1), BLOOM(2), 0, when not looking for cont

◆ minL

int _iparam_trimFilter::minL

minimum read length accepted before discarding a read

◆ minQ

int _iparam_trimFilter::minQ

minimum quality threshold

◆ nlowQ

int _iparam_trimFilter::nlowQ

maximum number of lowQ bases accepted before discarding

◆ Oprefix

char* _iparam_trimFilter::Oprefix

Output files prefix for single str (PATH/prefix)

◆ percent

int _iparam_trimFilter::percent

percentage of lowQ bases allowed in a read

◆ ptr_bfkmer

Bfkmer* _iparam_trimFilter::ptr_bfkmer

bloom filter kmer structure

◆ score

double _iparam_trimFilter::score

score threshold for matching reads in sequences

◆ trimN

int _iparam_trimFilter::trimN

◆ trimQ

int _iparam_trimFilter::trimQ

◆ uncompress

bool _iparam_trimFilter::uncompress

true if output uncompressed, false otherwise


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