Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcsamfile.pyx @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 # cython: embedsignature=True |
| jpayne@69 | 2 # cython: profile=True |
| jpayne@69 | 3 # adds doc-strings for sphinx |
| jpayne@69 | 4 import tempfile |
| jpayne@69 | 5 import os |
| jpayne@69 | 6 import sys |
| jpayne@69 | 7 import types |
| jpayne@69 | 8 import itertools |
| jpayne@69 | 9 import struct |
| jpayne@69 | 10 import ctypes |
| jpayne@69 | 11 import collections |
| jpayne@69 | 12 import re |
| jpayne@69 | 13 import platform |
| jpayne@69 | 14 import warnings |
| jpayne@69 | 15 from cpython cimport PyErr_SetString, \ |
| jpayne@69 | 16 PyBytes_Check, \ |
| jpayne@69 | 17 PyUnicode_Check, \ |
| jpayne@69 | 18 PyBytes_FromStringAndSize |
| jpayne@69 | 19 |
| jpayne@69 | 20 from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment |
| jpayne@69 | 21 |
| jpayne@69 | 22 |
| jpayne@69 | 23 cdef class Samfile(AlignmentFile): |
| jpayne@69 | 24 '''Deprecated alternative for :class:`~pysam.AlignmentFile` |
| jpayne@69 | 25 |
| jpayne@69 | 26 Added for backwards compatibility with pysam <= 0.8.0 |
| jpayne@69 | 27 ''' |
| jpayne@69 | 28 pass |
| jpayne@69 | 29 |
| jpayne@69 | 30 |
| jpayne@69 | 31 cdef class AlignedRead(AlignedSegment): |
| jpayne@69 | 32 '''Deprecated alternative for :class:`~pysam.AlignedSegment` |
| jpayne@69 | 33 |
| jpayne@69 | 34 Added for backwards compatibility with pysam <= 0.8.0 |
| jpayne@69 | 35 ''' |
| jpayne@69 | 36 pass |
| jpayne@69 | 37 |
| jpayne@69 | 38 |
| jpayne@69 | 39 __all__ = ['Samfile', 'AlignedRead'] |
| jpayne@69 | 40 |
| jpayne@69 | 41 |