#include <stdio.h>
#include <unistd.h>
#include <math.h>
+#include <inttypes.h>
#include "sam_header.h"
#include "sam.h"
#include "faidx.h"
// data passed to the bam_fetch callback is encapsulated in this struct.
typedef struct {
bam_header_t *header;
- int *count;
+ int64_t *count; // int does overflow for very big BAMs
} count_func_data_t;
typedef khash_t(rg) *rghash_t;
{
int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
int of_type = BAM_OFDEC, is_long_help = 0, n_threads = 0;
- int count = 0;
+ int64_t count = 0;
samfile_t *in = 0, *out = 0;
char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0, *q;
}
view_end:
- if (is_count && ret == 0) {
- printf("%d\n", count);
- }
+ if (is_count && ret == 0)
+ printf("%" PRId64 "\n", count);
+
// close files, free and return
free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
if (g_bed) bed_destroy(g_bed);