James Taylor avatar James Taylor committed 2392f72

Backed out changeset c1e165e97419, bgzf is still useful.

Comments (0)

Files changed (8)

 *.kpf
 
 # windows shortcuts
-*.lnk
-
-# nose egg
-nose*.egg
+*.lnk

lib/bx/misc/bgzf.c

+/* Generated by Cython 0.12 on Sat Jan  9 15:02:16 2010 */
+
+#define PY_SSIZE_T_CLEAN
+#include "Python.h"
+#include "structmember.h"
+#ifndef Py_PYTHON_H
+    #error Python headers needed to compile C extensions, please install development version of Python.
+#else
+#ifndef PY_LONG_LONG
+  #define PY_LONG_LONG LONG_LONG
+#endif
+#ifndef DL_EXPORT
+  #define DL_EXPORT(t) t
+#endif
+#if PY_VERSION_HEX < 0x02040000
+  #define METH_COEXIST 0
+  #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type)
+  #define PyDict_Contains(d,o)   PySequence_Contains(d,o)
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+#if PY_VERSION_HEX < 0x02050000
+  typedef int Py_ssize_t;
+  #define PY_SSIZE_T_MAX INT_MAX
+  #define PY_SSIZE_T_MIN INT_MIN
+  #define PY_FORMAT_SIZE_T ""
+  #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
+  #define PyInt_AsSsize_t(o)   PyInt_AsLong(o)
+  #define PyNumber_Index(o)    PyNumber_Int(o)
+  #define PyIndex_Check(o)     PyNumber_Check(o)
+#endif
+#if PY_VERSION_HEX < 0x02060000
+  #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
+  #define Py_TYPE(ob)   (((PyObject*)(ob))->ob_type)
+  #define Py_SIZE(ob)   (((PyVarObject*)(ob))->ob_size)
+  #define PyVarObject_HEAD_INIT(type, size) \
+          PyObject_HEAD_INIT(type) size,
+  #define PyType_Modified(t)
+
+  typedef struct {
+       void *buf;
+       PyObject *obj;
+       Py_ssize_t len;
+       Py_ssize_t itemsize;
+       int readonly;
+       int ndim;
+       char *format;
+       Py_ssize_t *shape;
+       Py_ssize_t *strides;
+       Py_ssize_t *suboffsets;
+       void *internal;
+  } Py_buffer;
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+  #define PyBUF_WRITABLE 0x0001
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+  #define Py_TPFLAGS_CHECKTYPES 0
+  #define Py_TPFLAGS_HAVE_INDEX 0
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+#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
+  #define Py_TPFLAGS_HAVE_NEWBUFFER 0
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+  #define PyString_Type                PyUnicode_Type
+  #define PyString_CheckExact          PyUnicode_CheckExact
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+  #define PyBytes_CheckExact           PyString_CheckExact
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+#if PY_MAJOR_VERSION >= 3
+  #define PyInt_Type                   PyLong_Type
+  #define PyInt_Check(op)              PyLong_Check(op)
+  #define PyInt_CheckExact(op)         PyLong_CheckExact(op)
+  #define PyInt_FromString             PyLong_FromString
+  #define PyInt_FromUnicode            PyLong_FromUnicode
+  #define PyInt_FromLong               PyLong_FromLong
+  #define PyInt_FromSize_t             PyLong_FromSize_t
+  #define PyInt_FromSsize_t            PyLong_FromSsize_t
+  #define PyInt_AsLong                 PyLong_AsLong
+  #define PyInt_AS_LONG                PyLong_AS_LONG
+  #define PyInt_AsSsize_t              PyLong_AsSsize_t
+  #define PyInt_AsUnsignedLongMask     PyLong_AsUnsignedLongMask
+  #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
+  #define __Pyx_PyNumber_Divide(x,y)         PyNumber_TrueDivide(x,y)
+  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceTrueDivide(x,y)
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+    #define __stdcall
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+  #endif
+  #ifndef __fastcall
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+  #define _USE_MATH_DEFINES
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+  #define __Pyx_GetAttrString(o,n)   PyObject_GetAttrString((o),((char *)(n)))
+  #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
+  #define __Pyx_DelAttrString(o,n)   PyObject_DelAttrString((o),((char *)(n)))
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+  #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
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+#endif
+#ifdef __cplusplus
+#define __PYX_EXTERN_C extern "C"
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+#define __PYX_EXTERN_C extern
+#endif
+#include <math.h>
+#define __PYX_HAVE_API__bx__misc__bgzf
+#include "bgzf.h"
+
+#ifdef __GNUC__
+#define INLINE __inline__
+#elif _WIN32
+#define INLINE __inline
+#else
+#define INLINE 
+#endif
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+#define __Pyx_PyBytes_AsUString(s)        ((unsigned char*) __Pyx_PyBytes_AsString(s))
+
+#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
+static INLINE int __Pyx_PyObject_IsTrue(PyObject*);
+static INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
+
+#if !defined(T_PYSSIZET)
+#if PY_VERSION_HEX < 0x02050000
+#define T_PYSSIZET T_INT
+#elif !defined(T_LONGLONG)
+#define T_PYSSIZET \
+        ((sizeof(Py_ssize_t) == sizeof(int))  ? T_INT  : \
+        ((sizeof(Py_ssize_t) == sizeof(long)) ? T_LONG : -1))
+#else
+#define T_PYSSIZET \
+        ((sizeof(Py_ssize_t) == sizeof(int))          ? T_INT      : \
+        ((sizeof(Py_ssize_t) == sizeof(long))         ? T_LONG     : \
+        ((sizeof(Py_ssize_t) == sizeof(PY_LONG_LONG)) ? T_LONGLONG : -1)))
+#endif
+#endif
+
+
+#if !defined(T_ULONGLONG)
+#define __Pyx_T_UNSIGNED_INT(x) \
+        ((sizeof(x) == sizeof(unsigned char))  ? T_UBYTE : \
+        ((sizeof(x) == sizeof(unsigned short)) ? T_USHORT : \
+        ((sizeof(x) == sizeof(unsigned int))   ? T_UINT : \
+        ((sizeof(x) == sizeof(unsigned long))  ? T_ULONG : -1))))
+#else
+#define __Pyx_T_UNSIGNED_INT(x) \
+        ((sizeof(x) == sizeof(unsigned char))  ? T_UBYTE : \
+        ((sizeof(x) == sizeof(unsigned short)) ? T_USHORT : \
+        ((sizeof(x) == sizeof(unsigned int))   ? T_UINT : \
+        ((sizeof(x) == sizeof(unsigned long))  ? T_ULONG : \
+        ((sizeof(x) == sizeof(unsigned PY_LONG_LONG)) ? T_ULONGLONG : -1)))))
+#endif
+#if !defined(T_LONGLONG)
+#define __Pyx_T_SIGNED_INT(x) \
+        ((sizeof(x) == sizeof(char))  ? T_BYTE : \
+        ((sizeof(x) == sizeof(short)) ? T_SHORT : \
+        ((sizeof(x) == sizeof(int))   ? T_INT : \
+        ((sizeof(x) == sizeof(long))  ? T_LONG : -1))))
+#else
+#define __Pyx_T_SIGNED_INT(x) \
+        ((sizeof(x) == sizeof(char))  ? T_BYTE : \
+        ((sizeof(x) == sizeof(short)) ? T_SHORT : \
+        ((sizeof(x) == sizeof(int))   ? T_INT : \
+        ((sizeof(x) == sizeof(long))  ? T_LONG : \
+        ((sizeof(x) == sizeof(PY_LONG_LONG))   ? T_LONGLONG : -1)))))
+#endif
+
+#define __Pyx_T_FLOATING(x) \
+        ((sizeof(x) == sizeof(float)) ? T_FLOAT : \
+        ((sizeof(x) == sizeof(double)) ? T_DOUBLE : -1))
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+#if !defined(T_SIZET)
+#if !defined(T_ULONGLONG)
+#define T_SIZET \
+        ((sizeof(size_t) == sizeof(unsigned int))  ? T_UINT  : \
+        ((sizeof(size_t) == sizeof(unsigned long)) ? T_ULONG : -1))
+#else
+#define T_SIZET \
+        ((sizeof(size_t) == sizeof(unsigned int))          ? T_UINT      : \
+        ((sizeof(size_t) == sizeof(unsigned long))         ? T_ULONG     : \
+        ((sizeof(size_t) == sizeof(unsigned PY_LONG_LONG)) ? T_ULONGLONG : -1)))
+#endif
+#endif
+
+static INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
+static INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
+static INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
+
+#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+
+
+#ifdef __GNUC__
+/* Test for GCC > 2.95 */
+#if __GNUC__ > 2 ||               (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) 
+#define likely(x)   __builtin_expect(!!(x), 1)
+#define unlikely(x) __builtin_expect(!!(x), 0)
+#else /* __GNUC__ > 2 ... */
+#define likely(x)   (x)
+#define unlikely(x) (x)
+#endif /* __GNUC__ > 2 ... */
+#else /* __GNUC__ */
+#define likely(x)   (x)
+#define unlikely(x) (x)
+#endif /* __GNUC__ */
+    
+static PyObject *__pyx_m;
+static PyObject *__pyx_b;
+static PyObject *__pyx_empty_tuple;
+static PyObject *__pyx_empty_bytes;
+static int __pyx_lineno;
+static int __pyx_clineno = 0;
+static const char * __pyx_cfilenm= __FILE__;
+static const char *__pyx_filename;
+static const char **__pyx_f;
+
+
+typedef unsigned PY_LONG_LONG __pyx_t_2bx_4misc_4bgzf_int64_t;
+
+/* Type declarations */
+
+/* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":20
+ *     int64_t bgzf_seek( BGZF * fp, int64_t pos, int where )
+ * 
+ * cdef class BGZFFile( object ):             # <<<<<<<<<<<<<<
+ *     cdef BGZF * bgzf
+ *     def __init__( self, path, mode="r" ):
+ */
+
+struct __pyx_obj_2bx_4misc_4bgzf_BGZFFile {
+  PyObject_HEAD
+  BGZF *bgzf;
+};
+
+#ifndef CYTHON_REFNANNY
+  #define CYTHON_REFNANNY 0
+#endif
+
+#if CYTHON_REFNANNY
+  typedef struct {
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+    void (*DECREF)(void*, PyObject*, int);
+    void (*GOTREF)(void*, PyObject*, int);
+    void (*GIVEREF)(void*, PyObject*, int);
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+    if (!m) goto end;
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+  #define __Pyx_RefNannyFinishContext()
+  #define __Pyx_INCREF(r) Py_INCREF(r)
+  #define __Pyx_DECREF(r) Py_DECREF(r)
+  #define __Pyx_GOTREF(r)
+  #define __Pyx_GIVEREF(r)
+  #define __Pyx_XDECREF(r) Py_XDECREF(r)
+#endif /* CYTHON_REFNANNY */
+#define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);} } while(0)
+#define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r);} } while(0)
+
+static void __Pyx_RaiseDoubleKeywordsError(
+    const char* func_name, PyObject* kw_name); /*proto*/
+
+static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
+    Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
+
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],     PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,     const char* function_name); /*proto*/
+
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
+
+static INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+static INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
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+static INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
+
+static INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
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+static INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);
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+static INLINE char __Pyx_PyInt_AsChar(PyObject *);
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+static INLINE short __Pyx_PyInt_AsShort(PyObject *);
+
+static INLINE int __Pyx_PyInt_AsInt(PyObject *);
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+static INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);
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+static INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);
+
+static INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);
+
+static INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);
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+static INLINE long __Pyx_PyInt_AsLong(PyObject *);
+
+static INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);
+
+static INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
+
+static INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
+
+static void __Pyx_AddTraceback(const char *funcname); /*proto*/
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+/* Module declarations from bx.misc.bgzf */
+
+static PyTypeObject *__pyx_ptype_2bx_4misc_4bgzf_BGZFFile = 0;
+#define __Pyx_MODULE_NAME "bx.misc.bgzf"
+int __pyx_module_is_main_bx__misc__bgzf = 0;
+
+/* Implementation of bx.misc.bgzf */
+static PyObject *__pyx_builtin_IOError;
+static char __pyx_k_1[] = "Could not open file";
+static char __pyx_k_2[] = "\nSeekable access to BGZ files based on samtools code. Does not yet implement\ncomplete file-like interface.\n";
+static char __pyx_k__r[] = "r";
+static char __pyx_k__pos[] = "pos";
+static char __pyx_k__bgzf[] = "bgzf";
+static char __pyx_k__mode[] = "mode";
+static char __pyx_k__path[] = "path";
+static char __pyx_k__where[] = "where";
+static char __pyx_k__IOError[] = "IOError";
+static char __pyx_k____main__[] = "__main__";
+static char __pyx_k____test__[] = "__test__";
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+static PyObject *__pyx_n_s__IOError;
+static PyObject *__pyx_n_s____main__;
+static PyObject *__pyx_n_s____test__;
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+static PyObject *__pyx_n_s__mode;
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+static PyObject *__pyx_n_s__r;
+static PyObject *__pyx_n_s__where;
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+/* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":22
+ * cdef class BGZFFile( object ):
+ *     cdef BGZF * bgzf
+ *     def __init__( self, path, mode="r" ):             # <<<<<<<<<<<<<<
+ *         self.bgzf = bgzf_open( path, mode )
+ *         if not self.bgzf:
+ */
+
+static int __pyx_pf_2bx_4misc_4bgzf_8BGZFFile___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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+  /* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":23
+ *     cdef BGZF * bgzf
+ *     def __init__( self, path, mode="r" ):
+ *         self.bgzf = bgzf_open( path, mode )             # <<<<<<<<<<<<<<
+ *         if not self.bgzf:
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+  &__pyx_tp_as_mapping_BGZFFile, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer_BGZFFile, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+  0, /*tp_doc*/
+  0, /*tp_traverse*/
+  0, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_2bx_4misc_4bgzf_BGZFFile, /*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*/
+  __pyx_pf_2bx_4misc_4bgzf_8BGZFFile___init__, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_2bx_4misc_4bgzf_BGZFFile, /*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 PyMethodDef __pyx_methods[] = {
+  {0, 0, 0, 0}
+};
+
+static void __pyx_init_filenames(void); /*proto*/
+
+#if PY_MAJOR_VERSION >= 3
+static struct PyModuleDef __pyx_moduledef = {
+    PyModuleDef_HEAD_INIT,
+    __Pyx_NAMESTR("bgzf"),
+    __Pyx_DOCSTR(__pyx_k_2), /* m_doc */
+    -1, /* m_size */
+    __pyx_methods /* m_methods */,
+    NULL, /* m_reload */
+    NULL, /* m_traverse */
+    NULL, /* m_clear */
+    NULL /* m_free */
+};
+#endif
+
+static __Pyx_StringTabEntry __pyx_string_tab[] = {
+  {&__pyx_kp_s_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 0, 1, 0},
+  {&__pyx_n_s__IOError, __pyx_k__IOError, sizeof(__pyx_k__IOError), 0, 0, 1, 1},
+  {&__pyx_n_s____main__, __pyx_k____main__, sizeof(__pyx_k____main__), 0, 0, 1, 1},
+  {&__pyx_n_s____test__, __pyx_k____test__, sizeof(__pyx_k____test__), 0, 0, 1, 1},
+  {&__pyx_n_s__bgzf, __pyx_k__bgzf, sizeof(__pyx_k__bgzf), 0, 0, 1, 1},
+  {&__pyx_n_s__mode, __pyx_k__mode, sizeof(__pyx_k__mode), 0, 0, 1, 1},
+  {&__pyx_n_s__path, __pyx_k__path, sizeof(__pyx_k__path), 0, 0, 1, 1},
+  {&__pyx_n_s__pos, __pyx_k__pos, sizeof(__pyx_k__pos), 0, 0, 1, 1},
+  {&__pyx_n_s__r, __pyx_k__r, sizeof(__pyx_k__r), 0, 0, 1, 1},
+  {&__pyx_n_s__where, __pyx_k__where, sizeof(__pyx_k__where), 0, 0, 1, 1},
+  {0, 0, 0, 0, 0, 0, 0}
+};
+static int __Pyx_InitCachedBuiltins(void) {
+  __pyx_builtin_IOError = __Pyx_GetName(__pyx_b, __pyx_n_s__IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  return 0;
+  __pyx_L1_error:;
+  return -1;
+}
+
+static int __Pyx_InitGlobals(void) {
+  if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+  return 0;
+  __pyx_L1_error:;
+  return -1;
+}
+
+#if PY_MAJOR_VERSION < 3
+PyMODINIT_FUNC initbgzf(void); /*proto*/
+PyMODINIT_FUNC initbgzf(void)
+#else
+PyMODINIT_FUNC PyInit_bgzf(void); /*proto*/
+PyMODINIT_FUNC PyInit_bgzf(void)
+#endif
+{
+  PyObject *__pyx_t_1 = NULL;
+  #if CYTHON_REFNANNY
+  void* __pyx_refnanny = NULL;
+  __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
+  if (!__Pyx_RefNanny) {
+      PyErr_Clear();
+      __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny");
+      if (!__Pyx_RefNanny)
+          Py_FatalError("failed to import 'refnanny' module");
+  }
+  __pyx_refnanny = __Pyx_RefNanny->SetupContext("PyMODINIT_FUNC PyInit_bgzf(void)", __LINE__, __FILE__);
+  #endif
+  __pyx_init_filenames();
+  __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  #if PY_MAJOR_VERSION < 3
+  __pyx_empty_bytes = PyString_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  #else
+  __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  #endif
+  /*--- Library function declarations ---*/
+  /*--- Threads initialization code ---*/
+  #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
+  #ifdef WITH_THREAD /* Python build with threading support? */
+  PyEval_InitThreads();
+  #endif
+  #endif
+  /*--- Module creation code ---*/
+  #if PY_MAJOR_VERSION < 3
+  __pyx_m = Py_InitModule4(__Pyx_NAMESTR("bgzf"), __pyx_methods, __Pyx_DOCSTR(__pyx_k_2), 0, PYTHON_API_VERSION);
+  #else
+  __pyx_m = PyModule_Create(&__pyx_moduledef);
+  #endif
+  if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+  #if PY_MAJOR_VERSION < 3
+  Py_INCREF(__pyx_m);
+  #endif
+  __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
+  if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+  if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+  /*--- Initialize various global constants etc. ---*/
+  if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__pyx_module_is_main_bx__misc__bgzf) {
+    if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+  }
+  /*--- Builtin init code ---*/
+  if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  /*--- Global init code ---*/
+  /*--- Function export code ---*/
+  /*--- Type init code ---*/
+  if (PyType_Ready(&__pyx_type_2bx_4misc_4bgzf_BGZFFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "BGZFFile", (PyObject *)&__pyx_type_2bx_4misc_4bgzf_BGZFFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_2bx_4misc_4bgzf_BGZFFile = &__pyx_type_2bx_4misc_4bgzf_BGZFFile;
+  /*--- Type import code ---*/
+  /*--- Function import code ---*/
+  /*--- Execution code ---*/
+
+  /* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":1
+ * """             # <<<<<<<<<<<<<<
+ * Seekable access to BGZ files based on samtools code. Does not yet implement
+ * complete file-like interface.
+ */
+  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+  goto __pyx_L0;
+  __pyx_L1_error:;
+  __Pyx_XDECREF(__pyx_t_1);
+  if (__pyx_m) {
+    __Pyx_AddTraceback("init bx.misc.bgzf");
+    Py_DECREF(__pyx_m); __pyx_m = 0;
+  } else if (!PyErr_Occurred()) {
+    PyErr_SetString(PyExc_ImportError, "init bx.misc.bgzf");
+  }
+  __pyx_L0:;
+  __Pyx_RefNannyFinishContext();
+  #if PY_MAJOR_VERSION < 3
+  return;
+  #else
+  return __pyx_m;
+  #endif
+}
+
+static const char *__pyx_filenames[] = {
+  "bgzf.pyx",
+};
+
+/* Runtime support code */
+
+static void __pyx_init_filenames(void) {
+  __pyx_f = __pyx_filenames;
+}
+
+static void __Pyx_RaiseDoubleKeywordsError(
+    const char* func_name,
+    PyObject* kw_name)
+{
+    PyErr_Format(PyExc_TypeError,
+        #if PY_MAJOR_VERSION >= 3
+        "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
+        #else
+        "%s() got multiple values for keyword argument '%s'", func_name,
+        PyString_AS_STRING(kw_name));
+        #endif
+}
+
+static void __Pyx_RaiseArgtupleInvalid(
+    const char* func_name,
+    int exact,
+    Py_ssize_t num_min,
+    Py_ssize_t num_max,
+    Py_ssize_t num_found)
+{
+    Py_ssize_t num_expected;
+    const char *number, *more_or_less;
+
+    if (num_found < num_min) {
+        num_expected = num_min;
+        more_or_less = "at least";
+    } else {
+        num_expected = num_max;
+        more_or_less = "at most";
+    }
+    if (exact) {
+        more_or_less = "exactly";
+    }
+    number = (num_expected == 1) ? "" : "s";
+    PyErr_Format(PyExc_TypeError,
+        #if PY_VERSION_HEX < 0x02050000
+            "%s() takes %s %d positional argument%s (%d given)",
+        #else
+            "%s() takes %s %zd positional argument%s (%zd given)",
+        #endif
+        func_name, more_or_less, num_expected, number, num_found);
+}
+
+static int __Pyx_ParseOptionalKeywords(
+    PyObject *kwds,
+    PyObject **argnames[],
+    PyObject *kwds2,
+    PyObject *values[],
+    Py_ssize_t num_pos_args,
+    const char* function_name)
+{
+    PyObject *key = 0, *value = 0;
+    Py_ssize_t pos = 0;
+    PyObject*** name;
+    PyObject*** first_kw_arg = argnames + num_pos_args;
+
+    while (PyDict_Next(kwds, &pos, &key, &value)) {
+        name = first_kw_arg;
+        while (*name && (**name != key)) name++;
+        if (*name) {
+            values[name-argnames] = value;
+        } else {
+            #if PY_MAJOR_VERSION < 3
+            if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
+            #else
+            if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
+            #endif
+                goto invalid_keyword_type;
+            } else {
+                for (name = first_kw_arg; *name; name++) {
+                    #if PY_MAJOR_VERSION >= 3
+                    if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+                        PyUnicode_Compare(**name, key) == 0) break;
+                    #else
+                    if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+                        _PyString_Eq(**name, key)) break;
+                    #endif
+                }
+                if (*name) {
+                    values[name-argnames] = value;
+                } else {
+                    /* unexpected keyword found */
+                    for (name=argnames; name != first_kw_arg; name++) {
+                        if (**name == key) goto arg_passed_twice;
+                        #if PY_MAJOR_VERSION >= 3
+                        if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+                            PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
+                        #else
+                        if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+                            _PyString_Eq(**name, key)) goto arg_passed_twice;
+                        #endif
+                    }
+                    if (kwds2) {
+                        if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+                    } else {
+                        goto invalid_keyword;
+                    }
+                }
+            }
+        }
+    }
+    return 0;
+arg_passed_twice:
+    __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+    goto bad;
+invalid_keyword_type:
+    PyErr_Format(PyExc_TypeError,
+        "%s() keywords must be strings", function_name);
+    goto bad;
+invalid_keyword:
+    PyErr_Format(PyExc_TypeError,
+    #if PY_MAJOR_VERSION < 3
+        "%s() got an unexpected keyword argument '%s'",
+        function_name, PyString_AsString(key));
+    #else
+        "%s() got an unexpected keyword argument '%U'",
+        function_name, key);
+    #endif
+bad:
+    return -1;
+}
+
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
+    PyObject *result;
+    result = PyObject_GetAttr(dict, name);
+    if (!result)
+        PyErr_SetObject(PyExc_NameError, name);
+    return result;
+}
+
+static INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+    PyObject *tmp_type, *tmp_value, *tmp_tb;
+    PyThreadState *tstate = PyThreadState_GET();
+
+    tmp_type = tstate->curexc_type;
+    tmp_value = tstate->curexc_value;
+    tmp_tb = tstate->curexc_traceback;
+    tstate->curexc_type = type;
+    tstate->curexc_value = value;
+    tstate->curexc_traceback = tb;
+    Py_XDECREF(tmp_type);
+    Py_XDECREF(tmp_value);
+    Py_XDECREF(tmp_tb);
+}
+
+static INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+    PyThreadState *tstate = PyThreadState_GET();
+    *type = tstate->curexc_type;
+    *value = tstate->curexc_value;
+    *tb = tstate->curexc_traceback;
+
+    tstate->curexc_type = 0;
+    tstate->curexc_value = 0;
+    tstate->curexc_traceback = 0;
+}
+
+
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+    Py_XINCREF(type);
+    Py_XINCREF(value);
+    Py_XINCREF(tb);
+    /* First, check the traceback argument, replacing None with NULL. */
+    if (tb == Py_None) {
+        Py_DECREF(tb);
+        tb = 0;
+    }
+    else if (tb != NULL && !PyTraceBack_Check(tb)) {
+        PyErr_SetString(PyExc_TypeError,
+            "raise: arg 3 must be a traceback or None");
+        goto raise_error;
+    }
+    /* Next, replace a missing value with None */
+    if (value == NULL) {
+        value = Py_None;
+        Py_INCREF(value);
+    }
+    #if PY_VERSION_HEX < 0x02050000
+    if (!PyClass_Check(type))
+    #else
+    if (!PyType_Check(type))
+    #endif
+    {
+        /* Raising an instance.  The value should be a dummy. */
+        if (value != Py_None) {
+            PyErr_SetString(PyExc_TypeError,
+                "instance exception may not have a separate value");
+            goto raise_error;
+        }
+        /* Normalize to raise <class>, <instance> */
+        Py_DECREF(value);
+        value = type;
+        #if PY_VERSION_HEX < 0x02050000
+            if (PyInstance_Check(type)) {
+                type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+                Py_INCREF(type);
+            }
+            else {
+                type = 0;
+                PyErr_SetString(PyExc_TypeError,
+                    "raise: exception must be an old-style class or instance");
+                goto raise_error;
+            }
+        #else
+            type = (PyObject*) Py_TYPE(type);
+            Py_INCREF(type);
+            if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+                PyErr_SetString(PyExc_TypeError,
+                    "raise: exception class must be a subclass of BaseException");
+                goto raise_error;
+            }
+        #endif
+    }
+
+    __Pyx_ErrRestore(type, value, tb);
+    return;
+raise_error:
+    Py_XDECREF(value);
+    Py_XDECREF(type);
+    Py_XDECREF(tb);
+    return;
+}
+
+#else /* Python 3+ */
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+    if (tb == Py_None) {
+        tb = 0;
+    } else if (tb && !PyTraceBack_Check(tb)) {
+        PyErr_SetString(PyExc_TypeError,
+            "raise: arg 3 must be a traceback or None");
+        goto bad;
+    }
+    if (value == Py_None)
+        value = 0;
+
+    if (PyExceptionInstance_Check(type)) {
+        if (value) {
+            PyErr_SetString(PyExc_TypeError,
+                "instance exception may not have a separate value");
+            goto bad;
+        }
+        value = type;
+        type = (PyObject*) Py_TYPE(value);
+    } else if (!PyExceptionClass_Check(type)) {
+        PyErr_SetString(PyExc_TypeError,
+            "raise: exception class must be a subclass of BaseException");
+        goto bad;
+    }
+
+    PyErr_SetObject(type, value);
+
+    if (tb) {
+        PyThreadState *tstate = PyThreadState_GET();
+        PyObject* tmp_tb = tstate->curexc_traceback;
+        if (tb != tmp_tb) {
+            Py_INCREF(tb);
+            tstate->curexc_traceback = tb;
+            Py_XDECREF(tmp_tb);
+        }
+    }
+
+bad:
+    return;
+}
+#endif
+
+static INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
+    const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+    if (sizeof(unsigned char) < sizeof(long)) {
+        long val = __Pyx_PyInt_AsLong(x);
+        if (unlikely(val != (long)(unsigned char)val)) {
+            if (!unlikely(val == -1 && PyErr_Occurred())) {
+                PyErr_SetString(PyExc_OverflowError,
+                    (is_unsigned && unlikely(val < 0)) ?
+                    "can't convert negative value to unsigned char" :
+                    "value too large to convert to unsigned char");
+            }
+            return (unsigned char)-1;
+        }
+        return (unsigned char)val;
+    }
+    return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
+    const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+    if (sizeof(unsigned short) < sizeof(long)) {
+        long val = __Pyx_PyInt_AsLong(x);
+        if (unlikely(val != (long)(unsigned short)val)) {
+            if (!unlikely(val == -1 && PyErr_Occurred())) {
+                PyErr_SetString(PyExc_OverflowError,
+                    (is_unsigned && unlikely(val < 0)) ?
+                    "can't convert negative value to unsigned short" :
+                    "value too large to convert to unsigned short");
+            }
+            return (unsigned short)-1;
+        }
+        return (unsigned short)val;
+    }
+    return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
+    const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+    if (sizeof(unsigned int) < sizeof(long)) {
+        long val = __Pyx_PyInt_AsLong(x);
+        if (unlikely(val != (long)(unsigned int)val)) {
+            if (!unlikely(val == -1 && PyErr_Occurred())) {
+                PyErr_SetString(PyExc_OverflowError,
+                    (is_unsigned && unlikely(val < 0)) ?
+                    "can't convert negative value to unsigned int" :
+                    "value too large to convert to unsigned int");
+            }
+            return (unsigned int)-1;
+        }
+        return (unsigned int)val;
+    }
+    return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
+    const char neg_one = (char)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+    if (sizeof(char) < sizeof(long)) {
+        long val = __Pyx_PyInt_AsLong(x);
+        if (unlikely(val != (long)(char)val)) {
+            if (!unlikely(val == -1 && PyErr_Occurred())) {
+                PyErr_SetString(PyExc_OverflowError,
+                    (is_unsigned && unlikely(val < 0)) ?
+                    "can't convert negative value to char" :
+                    "value too large to convert to char");
+            }
+            return (char)-1;
+        }
+        return (char)val;
+    }
+    return (char)__Pyx_PyInt_AsLong(x);
+}
+
+static INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
+    const short neg_one = (short)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+    if (sizeof(short) < sizeof(long)) {
+        long val = __Pyx_PyInt_AsLong(x);
+        if (unlikely(val != (long)(short)val)) {
+            if (!unlikely(val == -1 && PyErr_Occurred())) {
+                PyErr_SetString(PyExc_OverflowError,
+                    (is_unsigned && unlikely(val < 0)) ?
+                    "can't convert negative value to short" :
+                    "value too large to convert to short");
+            }
+            return (short)-1;
+        }
+        return (short)val;
+    }
+    return (short)__Pyx_PyInt_AsLong(x);
+}
+
+static INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
+    const int neg_one = (int)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+    if (sizeof(int) < sizeof(long)) {
+        long val = __Pyx_PyInt_AsLong(x);
+        if (unlikely(val != (long)(int)val)) {
+            if (!unlikely(val == -1 && PyErr_Occurred())) {
+                PyErr_SetString(PyExc_OverflowError,
+                    (is_unsigned && unlikely(val < 0)) ?
+                    "can't convert negative value to int" :
+                    "value too large to convert to int");
+            }
+            return (int)-1;
+        }
+        return (int)val;
+    }
+    return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
+    const signed char neg_one = (signed char)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+    if (sizeof(signed char) < sizeof(long)) {
+        long val = __Pyx_PyInt_AsLong(x);
+        if (unlikely(val != (long)(signed char)val)) {
+            if (!unlikely(val == -1 && PyErr_Occurred())) {
+                PyErr_SetString(PyExc_OverflowError,
+                    (is_unsigned && unlikely(val < 0)) ?
+                    "can't convert negative value to signed char" :
+                    "value too large to convert to signed char");
+            }
+            return (signed char)-1;
+        }
+        return (signed char)val;
+    }
+    return (signed char)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
+    const signed short neg_one = (signed short)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+    if (sizeof(signed short) < sizeof(long)) {
+        long val = __Pyx_PyInt_AsLong(x);
+        if (unlikely(val != (long)(signed short)val)) {
+            if (!unlikely(val == -1 && PyErr_Occurred())) {
+                PyErr_SetString(PyExc_OverflowError,
+                    (is_unsigned && unlikely(val < 0)) ?
+                    "can't convert negative value to signed short" :
+                    "value too large to convert to signed short");
+            }
+            return (signed short)-1;
+        }
+        return (signed short)val;
+    }
+    return (signed short)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
+    const signed int neg_one = (signed int)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+    if (sizeof(signed int) < sizeof(long)) {
+        long val = __Pyx_PyInt_AsLong(x);
+        if (unlikely(val != (long)(signed int)val)) {
+            if (!unlikely(val == -1 && PyErr_Occurred())) {
+                PyErr_SetString(PyExc_OverflowError,
+                    (is_unsigned && unlikely(val < 0)) ?
+                    "can't convert negative value to signed int" :
+                    "value too large to convert to signed int");
+            }
+            return (signed int)-1;
+        }
+        return (signed int)val;
+    }
+    return (signed int)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
+    const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+    if (likely(PyInt_Check(x))) {
+        long val = PyInt_AS_LONG(x);
+        if (is_unsigned && unlikely(val < 0)) {
+            PyErr_SetString(PyExc_OverflowError,
+                            "can't convert negative value to unsigned long");
+            return (unsigned long)-1;
+        }
+        return (unsigned long)val;
+    } else
+#endif
+    if (likely(PyLong_Check(x))) {
+        if (is_unsigned) {
+            if (unlikely(Py_SIZE(x) < 0)) {
+                PyErr_SetString(PyExc_OverflowError,
+                                "can't convert negative value to unsigned long");
+                return (unsigned long)-1;
+            }
+            return PyLong_AsUnsignedLong(x);
+        } else {
+            return PyLong_AsLong(x);
+        }
+    } else {
+        unsigned long val;
+        PyObject *tmp = __Pyx_PyNumber_Int(x);
+        if (!tmp) return (unsigned long)-1;
+        val = __Pyx_PyInt_AsUnsignedLong(tmp);
+        Py_DECREF(tmp);
+        return val;
+    }
+}
+
+static INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
+    const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+    if (likely(PyInt_Check(x))) {
+        long val = PyInt_AS_LONG(x);
+        if (is_unsigned && unlikely(val < 0)) {
+            PyErr_SetString(PyExc_OverflowError,
+                            "can't convert negative value to unsigned PY_LONG_LONG");
+            return (unsigned PY_LONG_LONG)-1;
+        }
+        return (unsigned PY_LONG_LONG)val;
+    } else
+#endif
+    if (likely(PyLong_Check(x))) {
+        if (is_unsigned) {
+            if (unlikely(Py_SIZE(x) < 0)) {
+                PyErr_SetString(PyExc_OverflowError,
+                                "can't convert negative value to unsigned PY_LONG_LONG");
+                return (unsigned PY_LONG_LONG)-1;
+            }
+            return PyLong_AsUnsignedLongLong(x);
+        } else {
+            return PyLong_AsLongLong(x);
+        }
+    } else {
+        unsigned PY_LONG_LONG val;
+        PyObject *tmp = __Pyx_PyNumber_Int(x);
+        if (!tmp) return (unsigned PY_LONG_LONG)-1;
+        val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
+        Py_DECREF(tmp);
+        return val;
+    }
+}
+
+static INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
+    const long neg_one = (long)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+    if (likely(PyInt_Check(x))) {
+        long val = PyInt_AS_LONG(x);
+        if (is_unsigned && unlikely(val < 0)) {
+            PyErr_SetString(PyExc_OverflowError,
+                            "can't convert negative value to long");
+            return (long)-1;
+        }
+        return (long)val;
+    } else
+#endif
+    if (likely(PyLong_Check(x))) {
+        if (is_unsigned) {
+            if (unlikely(Py_SIZE(x) < 0)) {
+                PyErr_SetString(PyExc_OverflowError,
+                                "can't convert negative value to long");
+                return (long)-1;
+            }
+            return PyLong_AsUnsignedLong(x);
+        } else {
+            return PyLong_AsLong(x);
+        }
+    } else {
+        long val;
+        PyObject *tmp = __Pyx_PyNumber_Int(x);
+        if (!tmp) return (long)-1;
+        val = __Pyx_PyInt_AsLong(tmp);
+        Py_DECREF(tmp);
+        return val;
+    }
+}
+
+static INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
+    const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+    if (likely(PyInt_Check(x))) {
+        long val = PyInt_AS_LONG(x);
+        if (is_unsigned && unlikely(val < 0)) {
+            PyErr_SetString(PyExc_OverflowError,
+                            "can't convert negative value to PY_LONG_LONG");
+            return (PY_LONG_LONG)-1;
+        }
+        return (PY_LONG_LONG)val;
+    } else
+#endif
+    if (likely(PyLong_Check(x))) {
+        if (is_unsigned) {
+            if (unlikely(Py_SIZE(x) < 0)) {
+                PyErr_SetString(PyExc_OverflowError,
+                                "can't convert negative value to PY_LONG_LONG");
+                return (PY_LONG_LONG)-1;
+            }
+            return PyLong_AsUnsignedLongLong(x);
+        } else {
+            return PyLong_AsLongLong(x);
+        }
+    } else {
+        PY_LONG_LONG val;
+        PyObject *tmp = __Pyx_PyNumber_Int(x);
+        if (!tmp) return (PY_LONG_LONG)-1;
+        val = __Pyx_PyInt_AsLongLong(tmp);
+        Py_DECREF(tmp);
+        return val;
+    }
+}
+
+static INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
+    const signed long neg_one = (signed long)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+    if (likely(PyInt_Check(x))) {
+        long val = PyInt_AS_LONG(x);
+        if (is_unsigned && unlikely(val < 0)) {
+            PyErr_SetString(PyExc_OverflowError,
+                            "can't convert negative value to signed long");
+            return (signed long)-1;
+        }
+        return (signed long)val;
+    } else
+#endif
+    if (likely(PyLong_Check(x))) {
+        if (is_unsigned) {
+            if (unlikely(Py_SIZE(x) < 0)) {
+                PyErr_SetString(PyExc_OverflowError,
+                                "can't convert negative value to signed long");
+                return (signed long)-1;
+            }
+            return PyLong_AsUnsignedLong(x);
+        } else {
+            return PyLong_AsLong(x);
+        }
+    } else {
+        signed long val;
+        PyObject *tmp = __Pyx_PyNumber_Int(x);
+        if (!tmp) return (signed long)-1;
+        val = __Pyx_PyInt_AsSignedLong(tmp);
+        Py_DECREF(tmp);
+        return val;
+    }
+}
+
+static INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
+    const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+    if (likely(PyInt_Check(x))) {
+        long val = PyInt_AS_LONG(x);
+        if (is_unsigned && unlikely(val < 0)) {
+            PyErr_SetString(PyExc_OverflowError,
+                            "can't convert negative value to signed PY_LONG_LONG");
+            return (signed PY_LONG_LONG)-1;
+        }
+        return (signed PY_LONG_LONG)val;
+    } else
+#endif
+    if (likely(PyLong_Check(x))) {
+        if (is_unsigned) {
+            if (unlikely(Py_SIZE(x) < 0)) {
+                PyErr_SetString(PyExc_OverflowError,
+                                "can't convert negative value to signed PY_LONG_LONG");
+                return (signed PY_LONG_LONG)-1;
+            }
+            return PyLong_AsUnsignedLongLong(x);
+        } else {
+            return PyLong_AsLongLong(x);
+        }
+    } else {
+        signed PY_LONG_LONG val;
+        PyObject *tmp = __Pyx_PyNumber_Int(x);
+        if (!tmp) return (signed PY_LONG_LONG)-1;
+        val = __Pyx_PyInt_AsSignedLongLong(tmp);
+        Py_DECREF(tmp);
+        return val;
+    }
+}
+
+#include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+
+static void __Pyx_AddTraceback(const char *funcname) {
+    PyObject *py_srcfile = 0;
+    PyObject *py_funcname = 0;
+    PyObject *py_globals = 0;
+    PyCodeObject *py_code = 0;
+    PyFrameObject *py_frame = 0;
+
+    #if PY_MAJOR_VERSION < 3
+    py_srcfile = PyString_FromString(__pyx_filename);
+    #else
+    py_srcfile = PyUnicode_FromString(__pyx_filename);
+    #endif
+    if (!py_srcfile) goto bad;
+    if (__pyx_clineno) {
+        #if PY_MAJOR_VERSION < 3
+        py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+        #else
+        py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+        #endif
+    }
+    else {
+        #if PY_MAJOR_VERSION < 3
+        py_funcname = PyString_FromString(funcname);
+        #else
+        py_funcname = PyUnicode_FromString(funcname);
+        #endif
+    }
+    if (!py_funcname) goto bad;
+    py_globals = PyModule_GetDict(__pyx_m);
+    if (!py_globals) goto bad;
+    py_code = PyCode_New(
+        0,            /*int argcount,*/
+        #if PY_MAJOR_VERSION >= 3
+        0,            /*int kwonlyargcount,*/
+        #endif
+        0,            /*int nlocals,*/
+        0,            /*int stacksize,*/
+        0,            /*int flags,*/
+        __pyx_empty_bytes, /*PyObject *code,*/
+        __pyx_empty_tuple,  /*PyObject *consts,*/
+        __pyx_empty_tuple,  /*PyObject *names,*/
+        __pyx_empty_tuple,  /*PyObject *varnames,*/
+        __pyx_empty_tuple,  /*PyObject *freevars,*/
+        __pyx_empty_tuple,  /*PyObject *cellvars,*/
+        py_srcfile,   /*PyObject *filename,*/
+        py_funcname,  /*PyObject *name,*/
+        __pyx_lineno,   /*int firstlineno,*/
+        __pyx_empty_bytes  /*PyObject *lnotab*/
+    );
+    if (!py_code) goto bad;
+    py_frame = PyFrame_New(
+        PyThreadState_GET(), /*PyThreadState *tstate,*/
+        py_code,             /*PyCodeObject *code,*/
+        py_globals,          /*PyObject *globals,*/
+        0                    /*PyObject *locals*/
+    );
+    if (!py_frame) goto bad;
+    py_frame->f_lineno = __pyx_lineno;
+    PyTraceBack_Here(py_frame);
+bad:
+    Py_XDECREF(py_srcfile);
+    Py_XDECREF(py_funcname);
+    Py_XDECREF(py_code);
+    Py_XDECREF(py_frame);
+}
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
+    while (t->p) {
+        #if PY_MAJOR_VERSION < 3
+        if (t->is_unicode) {
+            *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
+        } else if (t->intern) {
+            *t->p = PyString_InternFromString(t->s);
+        } else {
+            *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
+        }
+        #else  /* Python 3+ has unicode identifiers */
+        if (t->is_unicode | t->is_str) {
+            if (t->intern) {
+                *t->p = PyUnicode_InternFromString(t->s);
+            } else if (t->encoding) {
+                *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
+            } else {
+                *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
+            }
+        } else {
+            *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
+        }
+        #endif
+        if (!*t->p)
+            return -1;
+        ++t;
+    }
+    return 0;
+}
+
+/* Type Conversion Functions */
+
+static INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
+   if (x == Py_True) return 1;
+   else if ((x == Py_False) | (x == Py_None)) return 0;
+   else return PyObject_IsTrue(x);
+}
+
+static INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
+  PyNumberMethods *m;
+  const char *name = NULL;
+  PyObject *res = NULL;
+#if PY_VERSION_HEX < 0x03000000
+  if (PyInt_Check(x) || PyLong_Check(x))
+#else
+  if (PyLong_Check(x))
+#endif
+    return Py_INCREF(x), x;
+  m = Py_TYPE(x)->tp_as_number;
+#if PY_VERSION_HEX < 0x03000000
+  if (m && m->nb_int) {
+    name = "int";
+    res = PyNumber_Int(x);
+  }
+  else if (m && m->nb_long) {
+    name = "long";
+    res = PyNumber_Long(x);
+  }
+#else
+  if (m && m->nb_int) {
+    name = "int";
+    res = PyNumber_Long(x);
+  }
+#endif
+  if (res) {
+#if PY_VERSION_HEX < 0x03000000
+    if (!PyInt_Check(res) && !PyLong_Check(res)) {
+#else
+    if (!PyLong_Check(res)) {
+#endif
+      PyErr_Format(PyExc_TypeError,
+                   "__%s__ returned non-%s (type %.200s)",
+                   name, name, Py_TYPE(res)->tp_name);
+      Py_DECREF(res);
+      return NULL;
+    }
+  }
+  else if (!PyErr_Occurred()) {
+    PyErr_SetString(PyExc_TypeError,
+                    "an integer is required");
+  }
+  return res;
+}
+
+static INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
+  Py_ssize_t ival;
+  PyObject* x = PyNumber_Index(b);
+  if (!x) return -1;
+  ival = PyInt_AsSsize_t(x);
+  Py_DECREF(x);
+  return ival;
+}
+
+static INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
+#if PY_VERSION_HEX < 0x02050000
+   if (ival <= LONG_MAX)
+       return PyInt_FromLong((long)ival);
+   else {
+       unsigned char *bytes = (unsigned char *) &ival;
+       int one = 1; int little = (int)*(unsigned char*)&one;
+       return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
+   }
+#else
+   return PyInt_FromSize_t(ival);
+#endif
+}
+
+static INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
+   unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
+   if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
+       return (size_t)-1;
+   } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
+       PyErr_SetString(PyExc_OverflowError,
+                       "value too large to convert to size_t");
+       return (size_t)-1;
+   }
+   return (size_t)val;
+}
+
+
+#endif /* Py_PYTHON_H */

lib/bx/misc/bgzf.pyx

+"""
+Seekable access to BGZ files based on samtools code. Does not yet implement
+complete file-like interface.
+"""
+
+ctypedef unsigned long long int64_t
+
+cdef extern from "Python.h":
+    char * PyString_AsString( object )
+    object PyString_FromStringAndSize( char *, int )
+
+cdef extern from "bgzf.h":
+    ctypedef struct BGZF
+    BGZF * bgzf_open( char * path, char * mode )
+    int bgzf_close( BGZF * fp )
+    int bgzf_read( BGZF * fp, void * data, int length )
+    int64_t bgzf_tell( BGZF * fp )
+    int64_t bgzf_seek( BGZF * fp, int64_t pos, int where )
+    
+cdef class BGZFFile( object ):
+    cdef BGZF * bgzf
+    def __init__( self, path, mode="r" ):
+        self.bgzf = bgzf_open( path, mode )
+        if not self.bgzf:
+            raise IOError( "Could not open file" )
+    def close( self ):
+        if self.bgzf:
+            bgzf_close( self.bgzf )
+    def read( self, int length ):
+        cdef object rval = PyString_FromStringAndSize( NULL, length )
+        bgzf_read( self.bgzf, PyString_AsString( rval ), length )
+        return rval
+    def tell( self ):
+        return bgzf_tell( self.bgzf )
+    def seek( self, int64_t pos, int where=0 ):
+        return bgzf_seek( self.bgzf, pos, where )

lib/bx/misc/bgzf_tests.py

+import bx.misc.bgzf
+
+def test_bgzf():
+    f = bx.misc.bgzf.BGZFFile( "test_data/bgzf_tests/test.txt.gz" )
+    assert f.read( 10 ) == "begin 644 "
+    print f.seek( 0 )
+    assert f.read( 10 ) == "begin 644 "
     extensions.append( Extension( "bx.seq._twobit", [ "lib/bx/seq/_twobit.pyx" ] ) )
     # Translation if character / integer strings 
     extensions.append( Extension( "bx._seqmapping", [ "lib/bx/_seqmapping.pyx" ] ) )
+    # BGZF
+    extensions.append( Extension( "bx.misc.bgzf",
+                                  [ "lib/bx/misc/bgzf.pyx", "src/samtools/bgzf.c" ],
+                                  include_dirs=[ "src/samtools"],
+                                  libraries=['z'] ) )
+
     
     # The following extensions won't (currently) compile on windows
     if platform.system() not in ( 'Microsoft', 'Windows' ):
                                       [ "lib/bx/align/sitemask/_cpg.pyx", 
                                         "lib/bx/align/sitemask/find_cpg.c" ] ) )
         
-        # Counting n-grams in integer strings
+        # Counting n-grams in inteber strings
         extensions.append( Extension( "bx.intseq.ngramcount", [ "lib/bx/intseq/ngramcount.pyx" ] ) )
 
         # Seekable access to bzip2 files

src/samtools/bgzf.c

+/* The MIT License
+
+   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+*/
+
+/*
+  2009-06-29 by lh3: cache recent uncompressed blocks.
+  2009-06-25 by lh3: optionally use my knetfile library to access file on a FTP.
+  2009-06-12 by lh3: support a mode string like "wu" where 'u' for uncompressed output */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <fcntl.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include "bgzf.h"
+
+#include "khash.h"
+typedef struct {
+	int size;
+	uint8_t *block;
+	int64_t end_offset;
+} cache_t;
+KHASH_MAP_INIT_INT64(cache, cache_t)
+
+#if defined(_WIN32) || defined(_MSC_VER)
+#define ftello(fp) ftell(fp)
+#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
+#else
+extern off_t ftello(FILE *stream);
+extern int fseeko(FILE *stream, off_t offset, int whence);
+#endif
+
+typedef int8_t bgzf_byte_t;
+
+static const int DEFAULT_BLOCK_SIZE = 64 * 1024;
+static const int MAX_BLOCK_SIZE = 64 * 1024;
+
+static const int BLOCK_HEADER_LENGTH = 18;
+static const int BLOCK_FOOTER_LENGTH = 8;
+
+static const int GZIP_ID1 = 31;
+static const int GZIP_ID2 = 139;
+static const int CM_DEFLATE = 8;
+static const int FLG_FEXTRA = 4;
+static const int OS_UNKNOWN = 255;
+static const int BGZF_ID1 = 66; // 'B'
+static const int BGZF_ID2 = 67; // 'C'
+static const int BGZF_LEN = 2;
+static const int BGZF_XLEN = 6; // BGZF_LEN+4
+
+static const int GZIP_WINDOW_BITS = -15; // no zlib header
+static const int Z_DEFAULT_MEM_LEVEL = 8;
+
+
+inline
+void
+packInt16(uint8_t* buffer, uint16_t value)
+{
+    buffer[0] = value;
+    buffer[1] = value >> 8;
+}
+
+inline
+int
+unpackInt16(const uint8_t* buffer)
+{
+    return (buffer[0] | (buffer[1] << 8));
+}
+
+inline
+void
+packInt32(uint8_t* buffer, uint32_t value)
+{
+    buffer[0] = value;
+    buffer[1] = value >> 8;
+    buffer[2] = value >> 16;
+    buffer[3] = value >> 24;
+}
+
+static inline
+int
+bgzf_min(int x, int y)
+{
+    return (x < y) ? x : y;
+}
+
+static
+void
+report_error(BGZF* fp, const char* message) {
+    fp->error = message;
+}
+
+static BGZF *bgzf_read_init()
+{
+	BGZF *fp;
+	fp = calloc(1, sizeof(BGZF));
+    fp->uncompressed_block_size = MAX_BLOCK_SIZE;
+    fp->uncompressed_block = malloc(MAX_BLOCK_SIZE);
+    fp->compressed_block_size = MAX_BLOCK_SIZE;
+    fp->compressed_block = malloc(MAX_BLOCK_SIZE);
+	fp->cache_size = 0;
+	fp->cache = kh_init(cache);
+	return fp;
+}
+
+static
+BGZF*
+open_read(int fd)
+{
+#ifdef _USE_KNETFILE
+    knetFile *file = knet_dopen(fd, "r");
+#else
+    FILE* file = fdopen(fd, "r");
+#endif
+    BGZF* fp;
+	if (file == 0) return 0;
+	fp = bgzf_read_init();
+    fp->file_descriptor = fd;
+    fp->open_mode = 'r';
+#ifdef _USE_KNETFILE
+    fp->x.fpr = file;
+#else
+    fp->file = file;
+#endif
+    return fp;
+}
+
+static
+BGZF*
+open_write(int fd, bool is_uncompressed)
+{
+    FILE* file = fdopen(fd, "w");
+    BGZF* fp;
+	if (file == 0) return 0;
+	fp = malloc(sizeof(BGZF));
+    fp->file_descriptor = fd;
+    fp->open_mode = 'w';
+    fp->owned_file = 0; fp->is_uncompressed = is_uncompressed;
+#ifdef _USE_KNETFILE
+    fp->x.fpw = file;
+#else
+    fp->file = file;
+#endif
+    fp->uncompressed_block_size = DEFAULT_BLOCK_SIZE;
+    fp->uncompressed_block = NULL;
+    fp->compressed_block_size = MAX_BLOCK_SIZE;
+    fp->compressed_block = malloc(MAX_BLOCK_SIZE);
+    fp->block_address = 0;
+    fp->block_offset = 0;
+    fp->block_length = 0;
+    fp->error = NULL;
+    return fp;
+}
+
+BGZF*
+bgzf_open(const char* __restrict path, const char* __restrict mode)
+{
+    BGZF* fp = NULL;
+    if (mode[0] == 'r' || mode[0] == 'R') { /* The reading mode is preferred. */
+#ifdef _USE_KNETFILE
+		knetFile *file = knet_open(path, mode);
+		if (file == 0) return 0;
+		fp = bgzf_read_init();
+		fp->file_descriptor = -1;
+		fp->open_mode = 'r';
+		fp->x.fpr = file;
+#else
+		int fd, oflag = O_RDONLY;
+#ifdef _WIN32
+		oflag |= O_BINARY;
+#endif
+		fd = open(path, oflag);
+		if (fd == -1) return 0;
+        fp = open_read(fd);
+#endif
+    } else if (mode[0] == 'w' || mode[0] == 'W') {
+		int fd, oflag = O_WRONLY | O_CREAT | O_TRUNC;
+#ifdef _WIN32
+		oflag |= O_BINARY;
+#endif
+		fd = open(path, oflag, 0666);
+		if (fd == -1) return 0;
+        fp = open_write(fd, strstr(mode, "u")? 1 : 0);
+    }
+    if (fp != NULL) {
+        fp->owned_file = 1;
+    }
+    return fp;
+}
+
+BGZF*
+bgzf_fdopen(int fd, const char * __restrict mode)
+{
+	if (fd == -1) return 0;
+    if (mode[0] == 'r' || mode[0] == 'R') {
+        return open_read(fd);
+    } else if (mode[0] == 'w' || mode[0] == 'W') {
+        return open_write(fd, strstr(mode, "u")? 1 : 0);
+    } else {
+        return NULL;
+    }
+}
+
+static
+int
+deflate_block(BGZF* fp, int block_length)
+{
+    // Deflate the block in fp->uncompressed_block into fp->compressed_block.
+    // Also adds an extra field that stores the compressed block length.
+
+    bgzf_byte_t* buffer = fp->compressed_block;
+    int buffer_size = fp->compressed_block_size;
+
+    // Init gzip header
+    buffer[0] = GZIP_ID1;
+    buffer[1] = GZIP_ID2;
+    buffer[2] = CM_DEFLATE;
+    buffer[3] = FLG_FEXTRA;
+    buffer[4] = 0; // mtime
+    buffer[5] = 0;
+    buffer[6] = 0;
+    buffer[7] = 0;
+    buffer[8] = 0;
+    buffer[9] = OS_UNKNOWN;
+    buffer[10] = BGZF_XLEN;
+    buffer[11] = 0;
+    buffer[12] = BGZF_ID1;
+    buffer[13] = BGZF_ID2;
+    buffer[14] = BGZF_LEN;
+    buffer[15] = 0;
+    buffer[16] = 0; // placeholder for block length
+    buffer[17] = 0;
+
+    // loop to retry for blocks that do not compress enough
+    int input_length = block_length;
+    int compressed_length = 0;
+    while (1) {
+		int compress_level = fp->is_uncompressed? 0 : Z_DEFAULT_COMPRESSION;
+        z_stream zs;
+        zs.zalloc = NULL;
+        zs.zfree = NULL;
+        zs.next_in = fp->uncompressed_block;
+        zs.avail_in = input_length;
+        zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
+        zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
+
+        int status = deflateInit2(&zs, compress_level, Z_DEFLATED,
+                                  GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
+        if (status != Z_OK) {
+            report_error(fp, "deflate init failed");
+            return -1;
+        }
+        status = deflate(&zs, Z_FINISH);
+        if (status != Z_STREAM_END) {
+            deflateEnd(&zs);
+            if (status == Z_OK) {
+                // Not enough space in buffer.
+                // Can happen in the rare case the input doesn't compress enough.
+                // Reduce the amount of input until it fits.
+                input_length -= 1024;
+                if (input_length <= 0) {
+                    // should never happen
+                    report_error(fp, "input reduction failed");
+                    return -1;
+                }
+                continue;
+            }
+            report_error(fp, "deflate failed");
+            return -1;