bam_import.c

#include <zlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include "htslib/kstring.h"
#include "bam.h"
#include "htslib/kseq.h"

KSTREAM_INIT(gzFile, gzread, 16384)

bam_header_t *sam_header_read2(const char *fn)
{
	bam_header_t *header;
	int c, dret, n_targets = 0;
	gzFile fp;
	kstream_t *ks;
	kstring_t *str;
	kstring_t samstr = { 0, 0, NULL };
	if (fn == 0) return 0;
	fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
	if (fp == 0) return 0;
	ks = ks_init(fp);
	str = (kstring_t*)calloc(1, sizeof(kstring_t));
	while (ks_getuntil(ks, 0, str, &dret) > 0) {
		ksprintf(&samstr, "@SQ\tSN:%s", str->s);
		ks_getuntil(ks, 0, str, &dret);
		ksprintf(&samstr, "\tLN:%d\n", atoi(str->s));
		n_targets++;
		if (dret != '\n')
			while ((c = ks_getc(ks)) != '\n' && c != -1);
	}
	ks_destroy(ks);
	gzclose(fp);
	free(str->s); free(str);
	header = sam_hdr_parse(samstr.l, samstr.s? samstr.s : "");
	free(samstr.s);
	fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", n_targets);
	return header;
}