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/** Test routine for reverse complementing Fastq files
*/
/*****************************************************************************
*****************************************************************************
* *
* Copyright (C) 2010 - 2014 Genome Research Ltd. *
* *
* Author: Hannes Ponstingl (hp3@sanger.ac.uk) *
* *
* This file is part of SMALT. *
* *
* SMALT is free software: you can redistribute it and/or modify it under *
* the terms of the GNU General Public License as published by the Free *
* Software Foundation, either version 3 of the License, or (at your *
* option) any later version. *
* *
* This program is distributed in the hope that it will be useful, but *
* WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU *
* General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License along *
* with this program. If not, see <http://www.gnu.org/licenses/>. *
* *
*****************************************************************************
*****************************************************************************/
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include "elib.h"
#include "sequence.h"
#define MAXNAMLEN 256
#define OUTPUT_LINEWIDTH 60
int main(int argc, char *argv[])
{
int errcode = ERRCODE_SUCCESS;
long ctr = 0L;
SeqIO *sfp_in, *sfp_out;
SeqFastq *seqp;
SeqCodec *codecp;
ErrMsg *errmsg = 0;
ERRMSG_CREATE(errmsg);
if (argc < 3) {
printf("usage: %s <fasta/fastq file [in]> <fasta/fastq file [out]>\n",argv[0]);
exit(0);
}
if (!(codecp = seqCodecCreate()))
ERRMSGNO(errmsg, ERRCODE_FAILURE);
if (!(seqp = seqFastqCreate(0,SEQTYP_UNKNOWN)))
ERRMSGNO(errmsg, ERRCODE_NOMEM);
sfp_in = seqIOopen(&errcode, argv[1], SEQIO_READ, 0);
if (!sfp_in) ERRMSGNO(errmsg, errcode);
sfp_out = seqIOopen(&errcode, argv[2], SEQIO_WRITE_FASTQ, 0);
if (!sfp_out) ERRMSGNO(errmsg, errcode);
while(!(seqIOstatus(sfp_in) || seqIOstatus(sfp_out))) {
if ((errcode = seqFastqRead(seqp, sfp_in)))
ERRMSGNO(errmsg, errcode);
if ((errcode = seqFastqReverse(seqp, codecp)))
ERRMSGNO(errmsg, errcode);
if ((errcode = seqFastqWrite(sfp_out, seqp, 0)))
ERRMSGNO(errmsg, errcode);
ctr++;
}
printf("Revese complement of %li sequences.\n", ctr);
if (seqIOstatus(sfp_in) != ERRCODE_EOF) ERRMSGNO(errmsg, seqIOstatus(sfp_in));
if (seqIOstatus(sfp_out)) ERRMSGNO(errmsg, seqIOstatus(sfp_out));
seqIOclose(sfp_out);
seqIOclose(sfp_in);
seqFastqDelete(seqp);
seqCodecDelete(codecp);
ERRMSG_END(errmsg);
return ERRCODE_SUCCESS;
}
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