--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/py/biopython_modified_bgzf.py	Tue May 15 02:39:53 2018 -0400
@@ -0,0 +1,103 @@
+#!/usr/bin/env python
+# Copyright 2010-2013 by Peter Cock.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+""" ############################################################################
+#######                                                                  #######
+#######    06/02/2015:                                                   #######
+#######        - I picked out the bits and pieces of code needed         #######
+#######          to write BAM files, removed python 3.0 compatibility    #######
+#######                                                                  #######
+############################################################################ """
+
+import zlib
+import struct
+
+_bgzf_header = b"\x1f\x8b\x08\x04\x00\x00\x00\x00\x00\xff\x06\x00\x42\x43\x02\x00"
+_bgzf_eof    = b"\x1f\x8b\x08\x04\x00\x00\x00\x00\x00\xff\x06\x00\x42\x43\x02\x00\x1b\x00\x03\x00\x00\x00\x00\x00\x00\x00\x00\x00"
+
+class BgzfWriter(object):
+
+	def __init__(self, filename=None, mode="w", fileobj=None, compresslevel=6):
+		if fileobj:
+			assert filename is None
+			handle = fileobj
+		else:
+			if "w" not in mode.lower() \
+			and "a" not in mode.lower():
+				raise ValueError("Must use write or append mode, not %r" % mode)
+			if "a" in mode.lower():
+				handle = open(filename, "ab")
+			else:
+				handle = open(filename, "wb")
+		self._text = "b" not in mode.lower()
+		self._handle = handle
+		self._buffer = b""
+		self.compresslevel = compresslevel
+
+	def _write_block(self, block):
+		start_offset = self._handle.tell()
+		assert len(block) <= 65536
+		# Giving a negative window bits means no gzip/zlib headers, -15 used in samtools
+		c = zlib.compressobj(self.compresslevel,
+							 zlib.DEFLATED,
+							 -15,
+							 zlib.DEF_MEM_LEVEL,
+							 0)
+		compressed = c.compress(block) + c.flush()
+		del c
+		assert len(compressed) < 65536, "TODO - Didn't compress enough, try less data in this block"
+		crc = zlib.crc32(block)
+		# Should cope with a mix of Python platforms...
+		if crc < 0:
+			crc = struct.pack("<i", crc)
+		else:
+			crc = struct.pack("<I", crc)
+		bsize = struct.pack("<H", len(compressed) + 25)  # includes -1
+		crc = struct.pack("<I", zlib.crc32(block) & 0xffffffff)
+		uncompressed_length = struct.pack("<I", len(block))
+		data = _bgzf_header + bsize + compressed + crc + uncompressed_length
+		self._handle.write(data)
+
+	def write(self, data):
+		data_len = len(data)
+		if len(self._buffer) + data_len < 65536:
+			self._buffer += data
+			return
+		else:
+			self._buffer += data
+			while len(self._buffer) >= 65536:
+				self._write_block(self._buffer[:65536])
+				self._buffer = self._buffer[65536:]
+
+	def flush(self):
+		while len(self._buffer) >= 65536:
+			self._write_block(self._buffer[:65535])
+			self._buffer = self._buffer[65535:]
+		self._write_block(self._buffer)
+		self._buffer = b""
+		self._handle.flush()
+
+	def close(self):
+		"""Flush data, write 28 bytes empty BGZF EOF marker, and close the BGZF file."""
+		if self._buffer:
+			self.flush()
+		# samtools will look for a magic EOF marker, just a 28 byte empty BGZF block,
+		# and if it is missing warns the BAM file may be truncated. In addition to
+		# samtools writing this block, so too does bgzip - so we should too.
+		self._handle.write(_bgzf_eof)
+		self._handle.flush()
+		self._handle.close()
+
+	def __enter__(self):
+		return self
+
+	def __exit__(self, type, value, traceback):
+		self.close()
+
+
+if __name__ == "__main__":
+	pass