#include <zlib.h>

#include <stdio.h>

#include <stdlib.h>

#include <string.h>

#include <assert.h>

#include "bseq.h"

#include "kseq.h"

KSEQ_INIT2(, gzFile, gzread)

struct mm_bseq_file_s {

gzFile fp;

kseq_t *ks;

};

mm_bseq_file_t *mm_bseq_open(const char *fn)

{

mm_bseq_file_t *fp;

gzFile f;

f = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");

if (f == 0) return 0;

fp = (mm_bseq_file_t*)calloc(1, sizeof(mm_bseq_file_t));

fp->fp = f;

fp->ks = kseq_init(fp->fp);

return fp;

}

void mm_bseq_close(mm_bseq_file_t *fp)

{

kseq_destroy(fp->ks);

gzclose(fp->fp);

free(fp);

}

mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int chunk_size, int with_qual, int *n_)

{

int size = 0, m, n;

mm_bseq1_t *seqs;

kseq_t *ks = fp->ks;

m = n = 0; seqs = 0;

while (kseq_read(ks) >= 0) {

mm_bseq1_t *s;

assert(ks->seq.l <= INT32_MAX);

if (n >= m) {

m = m? m<<1 : 256;

seqs = (mm_bseq1_t*)realloc(seqs, m * sizeof(mm_bseq1_t));

}

s = &seqs[n];

s->name = strdup(ks->name.s);

s->seq = strdup(ks->seq.s);

s->qual = with_qual && ks->qual.l? strdup(ks->qual.s) : 0;

s->l_seq = ks->seq.l;

size += seqs[n++].l_seq;

if (size >= chunk_size) break;

}

*n_ = n;

return seqs;

}

int mm_bseq_eof(mm_bseq_file_t *fp)

{

return ks_eof(fp->ks->f);

}