64 lines
1.2 KiB
C
64 lines
1.2 KiB
C
#include <zlib.h>
|
|
#include <stdio.h>
|
|
#include <stdlib.h>
|
|
#include <string.h>
|
|
#include <assert.h>
|
|
#include "bseq.h"
|
|
#include "kseq.h"
|
|
KSEQ_INIT(gzFile, gzread)
|
|
|
|
struct bseq_file_s {
|
|
int is_eof;
|
|
gzFile fp;
|
|
kseq_t *ks;
|
|
};
|
|
|
|
bseq_file_t *bseq_open(const char *fn)
|
|
{
|
|
bseq_file_t *fp;
|
|
gzFile f;
|
|
f = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
|
|
if (f == 0) return 0;
|
|
fp = (bseq_file_t*)calloc(1, sizeof(bseq_file_t));
|
|
fp->fp = f;
|
|
fp->ks = kseq_init(fp->fp);
|
|
return fp;
|
|
}
|
|
|
|
void bseq_close(bseq_file_t *fp)
|
|
{
|
|
kseq_destroy(fp->ks);
|
|
gzclose(fp->fp);
|
|
free(fp);
|
|
}
|
|
|
|
bseq1_t *bseq_read(bseq_file_t *fp, int chunk_size, int *n_)
|
|
{
|
|
int size = 0, m, n;
|
|
bseq1_t *seqs;
|
|
kseq_t *ks = fp->ks;
|
|
m = n = 0; seqs = 0;
|
|
while (kseq_read(ks) >= 0) {
|
|
bseq1_t *s;
|
|
assert(ks->seq.l <= INT32_MAX);
|
|
if (n >= m) {
|
|
m = m? m<<1 : 256;
|
|
seqs = (bseq1_t*)realloc(seqs, m * sizeof(bseq1_t));
|
|
}
|
|
s = &seqs[n];
|
|
s->name = strdup(ks->name.s);
|
|
s->seq = strdup(ks->seq.s);
|
|
s->l_seq = ks->seq.l;
|
|
size += seqs[n++].l_seq;
|
|
if (size >= chunk_size) break;
|
|
}
|
|
if (n == 0) fp->is_eof = 1;
|
|
*n_ = n;
|
|
return seqs;
|
|
}
|
|
|
|
int bseq_eof(bseq_file_t *fp)
|
|
{
|
|
return fp->is_eof;
|
|
}
|