X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_sort.c;h=12b1b5455280e8d8a788a82929844083a4efd084;hp=9884f3d6273f680709ee0e44532a8371413fddf4;hb=049705238f6c2d4cdd79022e7bcf2cc7d83ba9c7;hpb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351

diff --git a/bam_sort.c b/bam_sort.c
index 9884f3d..12b1b54 100644
--- 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);