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/** Output stats on reads like read length
*/
/*****************************************************************************
*****************************************************************************
* *
* 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"
int main(int argc, char *argv[])
{
int errcode = ERRCODE_SUCCESS;
int ctr = 0;
char *infilnam;
const char *seqnam;
SEQLEN_t seqlen;
SeqIO *sfp_in;
SeqFastq *seqp;
ErrMsg *errmsg = 0;
ERRMSG_CREATE(errmsg);
if (argc < 2) {
printf("usage: %s <fasta/fastq file [in]>\n", argv[0]);
exit(0);
}
infilnam = argv[1];
if (!(seqp = seqFastqCreate(0,SEQTYP_UNKNOWN)))
ERRMSGNO(errmsg, ERRCODE_NOMEM);
sfp_in = seqIOopen(&errcode, infilnam, SEQIO_READ, 0);
if (!sfp_in) ERRMSGNO(errmsg, errcode);
while(!(seqIOstatus(sfp_in))) {
if ((errcode = seqFastqRead(seqp, sfp_in)))
ERRMSGNO(errmsg, errcode);
seqFastqGetSequence(seqp, &seqlen, NULL);
seqnam = seqFastqGetSeqName(seqp);
printf("%s %u\n", seqnam, seqlen);
ctr++;
}
if ((seqIOstatus(sfp_in)) && seqIOstatus(sfp_in) != ERRCODE_EOF)
ERRMSGNO(errmsg, seqIOstatus(sfp_in));
seqIOclose(sfp_in);
seqFastqDelete(seqp);
ERRMSG_END(errmsg);
return ERRCODE_SUCCESS;
}
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