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[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index c7a47747b4aba916911534591411ae0721b962a2..528309897bbf7c2a35bb4f2fa4727f522afb889e 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -14,7 +14,7 @@ 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 +128,7 @@ 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;
 
@@ -274,7 +274,7 @@ int main_samview(int argc, char *argv[])
 
 view_end:
        if (is_count && ret == 0) {
-               printf("%d\n", count);
+               printf("%ld\n", count); // compilers on some platforms may complain about printing int64_t with %ld
        }
        // close files, free and return
        free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);