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Merge commit 'upstream/0.1.8'
[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) {
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;
}
}
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);
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);
fnout = (char*)calloc(strlen(prefix) + 20, 1);
if (is_stdout) sprintf(fnout, "-");
else sprintf(fnout, "%s.bam", prefix);