X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam_view.c;h=7f3fdabc1ca581476246e64cca85fedc8b45207e;hb=7c3295ba455fdc9269156dd1246c92ea5df3efd4;hp=c7a47747b4aba916911534591411ae0721b962a2;hpb=0ab78ddb98818366103c11330526b8a2ea33a757;p=samtools.git

diff --git a/sam_view.c b/sam_view.c
index c7a4774..7f3fdab 100644
--- a/sam_view.c
+++ b/sam_view.c
@@ -3,6 +3,7 @@
 #include <stdio.h>
 #include <unistd.h>
 #include <math.h>
+#include <inttypes.h>
 #include "sam_header.h"
 #include "sam.h"
 #include "faidx.h"
@@ -14,7 +15,7 @@ KHASH_SET_INIT_STR(rg)
 // 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;
@@ -128,7 +129,7 @@ int main_samview(int argc, char *argv[])
 {
 	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;
 
@@ -273,9 +274,9 @@ int main_samview(int argc, char *argv[])
 	}
 
 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);