test sort cutsite

bin/hicstuff_io.py

@@ -1217,6 +1217,8 @@ def sort_pairs(in_file, out_file, keys, tmp_dir=None, threads=1, buffer="2G"):
             sort_cmd.append("--temporary-directory={0}".format(tmp_dir))
         if parallel_ok:
             sort_cmd.append("--parallel={0}".format(threads))
+        print(sort_cmd)
+        print(grep_proc)
         sort_proc = sp.Popen(sort_cmd, stdin=grep_proc.stdout, stdout=output)
         sort_proc.communicate()