FastqPuri
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trims/filter sequences after Quality, N's contaminations. More...
#include <stdio.h>
#include "Lmer.h"
#include "fq_read.h"
#include "defines.h"
#include "tree.h"
#include "bloom.h"
#include "adapters.h"
Go to the source code of this file.
Functions | |
int | trim_adapter (Fq_read *seq, Ad_seq *adap_list) |
trims sequence based on presence of N nucleotides More... | |
int | trim_sequenceN (Fq_read *seq) |
trims sequence based on presence of N nucleotides More... | |
int | trim_sequenceQ (Fq_read *seq) |
trims sequence based on lowQ base callings More... | |
bool | is_read_inTree (Tree *tree_ptr, Fq_read *seq) |
check if Lread is contained in tree. It computes the score for the read and its reverse complement; if one ot them exceeds the user selected threshold, it returns true. Otherwise, it returns false. More... | |
bool | is_read_inBloom (Bfilter *tree_ptr, Fq_read *seq, Bfkmer *ptr_Bfkmer) |
checks if a read is in Bloom filter. It computes the score for the read and returns true if it exceeds the user selected threshold. Returns false othersise. More... | |
int | Qtrim_global (Fq_read *seq, int left, int right, char type) |
trims left from the left and right from the right More... | |
trims/filter sequences after Quality, N's contaminations.
checks if a read is in Bloom filter. It computes the score for the read and returns true if it exceeds the user selected threshold. Returns false othersise.
ptr_bf | pointer to Bfilter |
seq | fastq read |
ptr_bfkmer | pointer to Procs_kmer structure (will store global) |
check if Lread is contained in tree. It computes the score for the read and its reverse complement; if one ot them exceeds the user selected threshold, it returns true. Otherwise, it returns false.
tree_ptr | pointer to Tree structure |
seq | fastq read |
int Qtrim_global | ( | Fq_read * | seq, |
int | left, | ||
int | right, | ||
char | type | ||
) |
trims left from the left and right from the right
seq | fastq read |
left | number of nucleotides to be trimmed from the left |
right | number of nucleotides to be trimmed from the right |
type | char indicating the type of trimming (Q,A). |
trims sequence based on presence of N nucleotides
if (adapter length < 16) -> search for seeds 8 nucleotides long else -> search for seeds 16 nucleotides long if (seed found) -> calculate score if score > threshold -> aligner found, trim / discard and exit. else -> search for seeds 8 nucleotides long
seq | pointer to Fq_read |
adap_list | array of Ad_seq |
int trim_sequenceN | ( | Fq_read * | seq | ) |
trims sequence based on presence of N nucleotides
seq | fastq read |
This function calls a different function depending on the method passed as input par_TF.trimN:
int trim_sequenceQ | ( | Fq_read * | seq | ) |
trims sequence based on lowQ base callings
seq | fastq read |
This function calls a different function depending on the method passed as input par_TF.trimQ: