minimap2/bseq.c

#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);
}