# Uploaded samtools version 0.1.14-1.

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index 38f15d655c253dc1f7e8cd50dd39c178c448f584..7aeccff3e1e8e61507c4983ce535de884d6bbcae 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -298,14 +298,19 @@ KSORT_INIT(sort, bam1_p, bam1_lt)
 
 static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout)
 {
-       char *name;
+       char *name, mode[3];
        int i;
        bamFile fp;
        ks_mergesort(sort, k, buf, 0);
        name = (char*)calloc(strlen(prefix) + 20, 1);
-       if (n >= 0) sprintf(name, "%s.%.4d.bam", prefix, n);
-       else sprintf(name, "%s.bam", prefix);
-       fp = is_stdout? bam_dopen(fileno(stdout), "w") : bam_open(name, "w");
+       if (n >= 0) {
+               sprintf(name, "%s.%.4d.bam", prefix, n);
+               strcpy(mode, "w1");
+       } else {
+               sprintf(name, "%s.bam", prefix);
+               strcpy(mode, "w");
+       }
+       fp = is_stdout? bam_dopen(fileno(stdout), mode) : bam_open(name, mode);
        if (fp == 0) {
                fprintf(stderr, "[sort_blocks] fail to create file %s.\n", name);
                free(name);