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#include "qes_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <zlib.h>
#include "kseq.h"
#ifdef ZLIB_FOUND
# include <zlib.h>
KSEQ_INIT(gzFile, gzread)
#else
# include <sys/stat.h>
# include <fcntl.h>
KSEQ_INIT(int, read)
#endif
int main(int argc, char *argv[])
{
if (argc < 2) return 1;
const char *fname = argv[1];
gzFile fp = gzopen(fname, "r");
kseq_t *kseq = kseq_init(fp);
ssize_t res = 0;
while((res = kseq_read(kseq)) > 0) {
if (kseq->qual.l < 1) {
// fasta
printf(">%s %s\n", kseq->name.s, kseq->comment.s);
puts(kseq->seq.s);
} else {
// fastq
printf("@%s %s\n", kseq->name.s, kseq->comment.s);
puts(kseq->seq.s);
puts("+");
puts(kseq->qual.s);
}
}
kseq_destroy(kseq);
gzclose(fp);
return 0;
}
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