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trimDS.h File Reference

trim adapters from double stranded data More...

#include "fq_read.h"
#include "defines.h"
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Classes

struct  _ds_adap
 structure containing an adapter pair (for read 1 and read 2) More...
 

Typedefs

typedef struct _ds_adap DS_adap
 structure containing an adapter pair (for read 1 and read 2)
 

Functions

DS_adap init_DSadap (char *ad1, char *ad2, int L1, int L2)
 initialization of a DS_adap structure More...
 
int trim_adapterDS (DS_adap *ptr_DSad, Fq_read *r1, Fq_read *r2)
 trim the sequences, discard them or keep them unchanged depending on them having adapters remnants. More...
 

Detailed Description

trim adapters from double stranded data

Author
Paula Perez paula.nosp@m.pere.nosp@m.zrubi.nosp@m.o@gm.nosp@m.ail.c.nosp@m.om
Date
05.10.2017

Function Documentation

◆ init_DSadap()

DS_adap init_DSadap ( char *  ad1,
char *  ad2,
int  L1,
int  L2 
)

initialization of a DS_adap structure

Parameters
ad1adapter 1 sequence
ad2adapter 2 sequence
L1adapter 1 sequence length
L2adapter 2 sequence length
Returns
initialized DS_adap structure

◆ trim_adapterDS()

int trim_adapterDS ( DS_adap ptr_DSad,
Fq_read r1,
Fq_read r2 
)

trim the sequences, discard them or keep them unchanged depending on them having adapters remnants.

Returns
0 if the read is to be discarded, 1 if left as is, 2 if trimmed. Reads are trimmed if 2 is returned.