jpayne@68: # cython: embedsignature=True
jpayne@68: # cython: profile=True
jpayne@68: # adds doc-strings for sphinx
jpayne@68: import tempfile
jpayne@68: import os
jpayne@68: import sys
jpayne@68: import types
jpayne@68: import itertools
jpayne@68: import struct
jpayne@68: import ctypes
jpayne@68: import collections
jpayne@68: import re
jpayne@68: import platform
jpayne@68: import warnings
jpayne@68: from cpython cimport PyErr_SetString, \
jpayne@68:     PyBytes_Check, \
jpayne@68:     PyUnicode_Check, \
jpayne@68:     PyBytes_FromStringAndSize
jpayne@68: 
jpayne@68: from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class Samfile(AlignmentFile):
jpayne@68:     '''Deprecated alternative for :class:`~pysam.AlignmentFile`
jpayne@68: 
jpayne@68:     Added for backwards compatibility with pysam <= 0.8.0
jpayne@68:     '''
jpayne@68:     pass
jpayne@68: 
jpayne@68: 
jpayne@68: cdef class AlignedRead(AlignedSegment):
jpayne@68:     '''Deprecated alternative for :class:`~pysam.AlignedSegment`
jpayne@68: 
jpayne@68:     Added for backwards compatibility with pysam <= 0.8.0
jpayne@68:     '''
jpayne@68:     pass
jpayne@68: 
jpayne@68: 
jpayne@68: __all__ = ['Samfile', 'AlignedRead']
jpayne@68: 
jpayne@68: