Copied from SVN revision 4710 and adapted to Git.

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index 9884f3d6273f680709ee0e44532a8371413fddf4..12b1b5455280e8d8a788a82929844083a4efd084 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -294,7 +294,7 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
                mem += ret;
                ++k;
                if (mem >= max_mem) {
-                       sort_blocks(n++, k, buf, prefix, header, is_stdout);
+                       sort_blocks(n++, k, buf, prefix, header, 0);
                        mem = 0; k = 0;
                }
        }
@@ -304,7 +304,7 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
        else { // then merge
                char **fns, *fnout;
                fprintf(stderr, "[bam_sort_core] merging from %d files...\n", n+1);
-               sort_blocks(n++, k, buf, prefix, header, is_stdout);
+               sort_blocks(n++, k, buf, prefix, header, 0);
                fnout = (char*)calloc(strlen(prefix) + 20, 1);
                if (is_stdout) sprintf(fnout, "-");
                else sprintf(fnout, "%s.bam", prefix);