Use byte replacement strategy

lib/galaxy/datatypes/sniff.py

@@ -112,8 +112,24 @@ def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload",
     i = 0
     with io.open(fd, mode="wb") as fp:
         with io.open(fname, mode="rb") as fi:
-            for i, line in enumerate(fi):
-                fp.write(b"%s\n" % line.rstrip(b"\r\n"))
+            line = b''
+            clean_line = b""
+            last_char = None
+            block = fi.read(block_size)
+            while block:
+                if last_char == "\r" and block.startswith(b"\n"):
+                    # last block ended with "\r", new block startswith "\n"
+                    # since we replace "\r" with "\n" in the previous iteration we skip the first byte
+                    block = block[1:]
+                # splitlines(True) splits at line terminators but keeps them so we can replace them
+                lines = block.splitlines(True)
+                for line in lines:
+                    clean_line = line.replace(b"\r\n", b"\n").replace(b"\r", b"\n")
+                    fp.write(clean_line)
+                last_char = util.unicodify(line, error='replace')[-1]
+                block = fi.read(block_size)
+            if not clean_line.endswith(b"\n"):
+                fp.write(b"\n")
     if in_place:
         shutil.move(temp_name, fname)
         # Return number of lines in file.