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-static PySequenceMethods __pyx_tp_as_sequence_AlignedRead = {
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- 0, /*sq_concat*/
- 0, /*sq_repeat*/
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- 0, /*sq_slice*/
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-static PyMappingMethods __pyx_tp_as_mapping_AlignedRead = {
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-static PyBufferProcs __pyx_tp_as_buffer_AlignedRead = {
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- 0, /*tp_getattr*/
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- &__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/
- __pyx_pf_9csamtools_11AlignedRead___hash__, /*tp_hash*/
- 0, /*tp_call*/
- __pyx_pf_9csamtools_11AlignedRead___str__, /*tp_str*/
- 0, /*tp_getattro*/
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- __Pyx_DOCSTR("AlignedRead()\n\n Class representing an aligned read. see SAM format specification for \n the meaning of fields (http://samtools.sourceforge.net/).\n\n This class stores a handle to the samtools C-structure representing\n an aligned read. Member read access is forwarded to the C-structure\n and converted into python objects. This implementation should be fast,\n as only the data needed is converted.\n\n For write access, the C-structure is updated in-place. This is\n not the most efficient way to build BAM entries, as the variable\n length data is concatenated and thus needs to resized if\n a field is updated. Furthermore, the BAM entry might be\n in an inconsistent state. The :meth:`~validate` method can\n be used to check if an entry is consistent.\n\n One issue to look out for is that the sequence should always\n be set *before* the quality scores. Setting the sequence will\n also erase any quality scores that were set previously.\n "), /*tp_doc*/
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-static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
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- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_17IteratorRowRegion___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion___next__)},
- {0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = {
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- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
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- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
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- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
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- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
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- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
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- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
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- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowRegion = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowRegion = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowRegion), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowRegion, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowRegion, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowRegion, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowRegion, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each iterator\n creates its own file handle by re-opening the\n file.\n\n Note that the index will be shared between \n samfile and the iterator.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorRowRegion, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_17IteratorRowRegion___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_17IteratorRowRegion___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowRegion, /*tp_methods*/
- 0, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowRegion, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowAll __pyx_vtable_9csamtools_IteratorRowAll;
-
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowAll *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
- if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o);
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- Py_DECREF(o); o = 0;
- }
- return o;
-}
-
-static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) {
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_14IteratorRowAll___dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
-}
-
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = {
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- {0, 0, 0, 0}
-};
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