FastqPuri
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trimFilter input parameters More...
#include <struct_trimFilter.h>
Public Attributes | |
char * | Ifq |
char * | Ifq2 |
char * | Ifa |
char * | Iidx |
char * | Iinfo |
char * | Oprefix |
bool | uncompress |
Adapter | ad |
Bfkmer * | ptr_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 |
trimFilter input parameters
Adapter _iparam_trimFilter::ad |
AdapterDS trimming parameters
int _iparam_trimFilter::globleft |
number of bases globally trimming from the left
int _iparam_trimFilter::globright |
number of bases globally trimming from the right
char* _iparam_trimFilter::Ifa |
Input fa file (containing contamination sequences)
char* _iparam_trimFilter::Ifq |
Input fq file single stranded
char* _iparam_trimFilter::Ifq2 |
Input fq file read 2
char* _iparam_trimFilter::Iidx |
Input index file (from an input.fa cont file)
char* _iparam_trimFilter::Iinfo |
Input index info file
bool _iparam_trimFilter::is_adapter |
true if filtering adapter sequences
bool _iparam_trimFilter::is_fa |
true if a fasta file was passed as a parameter
bool _iparam_trimFilter::is_idx |
true if an index file was passed as a parameter
int _iparam_trimFilter::kmersize |
kmersize to look for contamination
int _iparam_trimFilter::L |
read length
int _iparam_trimFilter::minL |
minimum read length accepted before discarding a read
int _iparam_trimFilter::minQ |
minimum quality threshold
int _iparam_trimFilter::nlowQ |
maximum number of lowQ bases accepted before discarding
char* _iparam_trimFilter::Oprefix |
Output files prefix for single str (PATH/prefix)
int _iparam_trimFilter::percent |
percentage of lowQ bases allowed in a read
Bfkmer* _iparam_trimFilter::ptr_bfkmer |
bloom filter kmer structure
double _iparam_trimFilter::score |
score threshold for matching reads in sequences
int _iparam_trimFilter::trimQ |
bool _iparam_trimFilter::uncompress |
true if output uncompressed, false otherwise