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#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)
extern unsigned char seq_nt4_table[256];
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;
}
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