Kanwei Li avatar Kanwei Li committed c1e165e

Remove bgzf as it's no longer planned to be used

Comments (0)

Files changed (8)

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

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)
-#endif
-#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;
-
-  #define PyBUF_SIMPLE 0
-  #define PyBUF_WRITABLE 0x0001
-  #define PyBUF_FORMAT 0x0004
-  #define PyBUF_ND 0x0008
-  #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
-  #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
-  #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
-  #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
-  #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
-
-#endif
-#if PY_MAJOR_VERSION < 3
-  #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
-#else
-  #define __Pyx_BUILTIN_MODULE_NAME "builtins"
-#endif
-#if PY_MAJOR_VERSION >= 3
-  #define Py_TPFLAGS_CHECKTYPES 0
-  #define Py_TPFLAGS_HAVE_INDEX 0
-#endif
-#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
-  #define Py_TPFLAGS_HAVE_NEWBUFFER 0
-#endif
-#if PY_MAJOR_VERSION >= 3
-  #define PyBaseString_Type            PyUnicode_Type
-  #define PyString_Type                PyUnicode_Type
-  #define PyString_CheckExact          PyUnicode_CheckExact
-#else
-  #define PyBytes_Type                 PyString_Type
-  #define PyBytes_CheckExact           PyString_CheckExact
-#endif
-#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)
-#else
-  #define __Pyx_PyNumber_Divide(x,y)         PyNumber_Divide(x,y)
-  #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceDivide(x,y)
-#endif
-#if PY_MAJOR_VERSION >= 3
-  #define PyMethod_New(func, self, klass) PyInstanceMethod_New(func)
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
-  #ifndef __stdcall
-    #define __stdcall
-  #endif
-  #ifndef __cdecl
-    #define __cdecl
-  #endif
-  #ifndef __fastcall
-    #define __fastcall
-  #endif
-#else
-  #define _USE_MATH_DEFINES
-#endif
-#if PY_VERSION_HEX < 0x02050000
-  #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)))
-#else
-  #define __Pyx_GetAttrString(o,n)   PyObject_GetAttrString((o),(n))
-  #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
-  #define __Pyx_DelAttrString(o,n)   PyObject_DelAttrString((o),(n))
-#endif
-#if PY_VERSION_HEX < 0x02050000
-  #define __Pyx_NAMESTR(n) ((char *)(n))
-  #define __Pyx_DOCSTR(n)  ((char *)(n))
-#else
-  #define __Pyx_NAMESTR(n) (n)
-  #define __Pyx_DOCSTR(n)  (n)
-#endif
-#ifdef __cplusplus
-#define __PYX_EXTERN_C extern "C"
-#else
-#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
-
-typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-
-/* Type Conversion Predeclarations */
-
-#if PY_MAJOR_VERSION < 3
-#define __Pyx_PyBytes_FromString          PyString_FromString
-#define __Pyx_PyBytes_FromStringAndSize   PyString_FromStringAndSize
-#define __Pyx_PyBytes_AsString            PyString_AsString
-#else
-#define __Pyx_PyBytes_FromString          PyBytes_FromString
-#define __Pyx_PyBytes_FromStringAndSize   PyBytes_FromStringAndSize
-#define __Pyx_PyBytes_AsString            PyBytes_AsString
-#endif
-
-#define __Pyx_PyBytes_FromUString(s)      __Pyx_PyBytes_FromString((char*)s)
-#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))
-
-#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 {
-    void (*INCREF)(void*, PyObject*, int);
-    void (*DECREF)(void*, PyObject*, int);
-    void (*GOTREF)(void*, PyObject*, int);
-    void (*GIVEREF)(void*, PyObject*, int);
-    void* (*SetupContext)(const char*, int, const char*);
-    void (*FinishContext)(void**);
-  } __Pyx_RefNannyAPIStruct;
-  static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
-  static __Pyx_RefNannyAPIStruct * __Pyx_RefNannyImportAPI(const char *modname) {
-    PyObject *m = NULL, *p = NULL;
-    void *r = NULL;
-    m = PyImport_ImportModule((char *)modname);
-    if (!m) goto end;
-    p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
-    if (!p) goto end;
-    r = PyLong_AsVoidPtr(p);
-  end:
-    Py_XDECREF(p);
-    Py_XDECREF(m);
-    return (__Pyx_RefNannyAPIStruct *)r;
-  }
-  #define __Pyx_RefNannySetupContext(name)           void *__pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
-  #define __Pyx_RefNannyFinishContext()           __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
-  #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
-  #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
-  #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
-  #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
-  #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r);} } while(0)
-#else
-  #define __Pyx_RefNannySetupContext(name)
-  #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*/
-
-static INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
-
-static INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
-
-static INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);
-
-static INLINE char __Pyx_PyInt_AsChar(PyObject *);
-
-static INLINE short __Pyx_PyInt_AsShort(PyObject *);
-
-static INLINE int __Pyx_PyInt_AsInt(PyObject *);
-
-static INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *);
-
-static INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);
-
-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 *);
-
-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__";
-static PyObject *__pyx_kp_s_1;
-static PyObject *__pyx_n_s__IOError;
-static PyObject *__pyx_n_s____main__;
-static PyObject *__pyx_n_s____test__;
-static PyObject *__pyx_n_s__bgzf;
-static PyObject *__pyx_n_s__mode;
-static PyObject *__pyx_n_s__path;
-static PyObject *__pyx_n_s__pos;
-static PyObject *__pyx_n_s__r;
-static PyObject *__pyx_n_s__where;
-
-/* "/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*/
-static int __pyx_pf_2bx_4misc_4bgzf_8BGZFFile___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
-  PyObject *__pyx_v_path = 0;
-  PyObject *__pyx_v_mode = 0;
-  int __pyx_r;
-  char *__pyx_t_1;
-  char *__pyx_t_2;
-  int __pyx_t_3;
-  PyObject *__pyx_t_4 = NULL;
-  PyObject *__pyx_t_5 = NULL;
-  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__path,&__pyx_n_s__mode,0};
-  __Pyx_RefNannySetupContext("__init__");
-  if (unlikely(__pyx_kwds)) {
-    Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
-    PyObject* values[2] = {0,0};
-    values[1] = ((PyObject *)__pyx_n_s__r);
-    switch (PyTuple_GET_SIZE(__pyx_args)) {
-      case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
-      case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
-      case  0: break;
-      default: goto __pyx_L5_argtuple_error;
-    }
-    switch (PyTuple_GET_SIZE(__pyx_args)) {
-      case  0:
-      values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__path);
-      if (likely(values[0])) kw_args--;
-      else goto __pyx_L5_argtuple_error;
-      case  1:
-      if (kw_args > 1) {
-        PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__mode);
-        if (unlikely(value)) { values[1] = value; kw_args--; }
-      }
-    }
-    if (unlikely(kw_args > 0)) {
-      if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-    }
-    __pyx_v_path = values[0];
-    __pyx_v_mode = values[1];
-  } else {
-    __pyx_v_mode = ((PyObject *)__pyx_n_s__r);
-    switch (PyTuple_GET_SIZE(__pyx_args)) {
-      case  2: __pyx_v_mode = PyTuple_GET_ITEM(__pyx_args, 1);
-      case  1: __pyx_v_path = PyTuple_GET_ITEM(__pyx_args, 0);
-      break;
-      default: goto __pyx_L5_argtuple_error;
-    }
-  }
-  goto __pyx_L4_argument_unpacking_done;
-  __pyx_L5_argtuple_error:;
-  __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-  __pyx_L3_error:;
-  __Pyx_AddTraceback("bx.misc.bgzf.BGZFFile.__init__");
-  return -1;
-  __pyx_L4_argument_unpacking_done:;
-  __Pyx_INCREF((PyObject *)__pyx_v_self);
-  __Pyx_INCREF(__pyx_v_path);
-  __Pyx_INCREF(__pyx_v_mode);
-
-  /* "/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:
- *             raise IOError( "Could not open file" )
- */
-  __pyx_t_1 = __Pyx_PyBytes_AsString(__pyx_v_path); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_t_2 = __Pyx_PyBytes_AsString(__pyx_v_mode); if (unlikely((!__pyx_t_2) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  ((struct __pyx_obj_2bx_4misc_4bgzf_BGZFFile *)__pyx_v_self)->bgzf = bgzf_open(__pyx_t_1, __pyx_t_2);
-
-  /* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":24
- *     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 ):
- */
-  __pyx_t_3 = (!(((struct __pyx_obj_2bx_4misc_4bgzf_BGZFFile *)__pyx_v_self)->bgzf != 0));
-  if (__pyx_t_3) {
-
-    /* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":25
- *         self.bgzf = bgzf_open( path, mode )
- *         if not self.bgzf:
- *             raise IOError( "Could not open file" )             # <<<<<<<<<<<<<<
- *     def close( self ):
- *         if self.bgzf:
- */
-    __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __Pyx_GOTREF(__pyx_t_4);
-    __Pyx_INCREF(((PyObject *)__pyx_kp_s_1));
-    PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_kp_s_1));
-    __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_1));
-    __pyx_t_5 = PyObject_Call(__pyx_builtin_IOError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __Pyx_GOTREF(__pyx_t_5);
-    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
-    __Pyx_Raise(__pyx_t_5, 0, 0);
-    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    goto __pyx_L6;
-  }
-  __pyx_L6:;
-
-  __pyx_r = 0;
-  goto __pyx_L0;
-  __pyx_L1_error:;
-  __Pyx_XDECREF(__pyx_t_4);
-  __Pyx_XDECREF(__pyx_t_5);
-  __Pyx_AddTraceback("bx.misc.bgzf.BGZFFile.__init__");
-  __pyx_r = -1;
-  __pyx_L0:;
-  __Pyx_DECREF((PyObject *)__pyx_v_self);
-  __Pyx_DECREF(__pyx_v_path);
-  __Pyx_DECREF(__pyx_v_mode);
-  __Pyx_RefNannyFinishContext();
-  return __pyx_r;
-}
-
-/* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":26
- *         if not self.bgzf:
- *             raise IOError( "Could not open file" )
- *     def close( self ):             # <<<<<<<<<<<<<<
- *         if self.bgzf:
- *             bgzf_close( self.bgzf )
- */
-
-static PyObject *__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_close(PyObject *__pyx_v_self, PyObject *unused); /*proto*/
-static PyObject *__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_close(PyObject *__pyx_v_self, PyObject *unused) {
-  PyObject *__pyx_r = NULL;
-  int __pyx_t_1;
-  __Pyx_RefNannySetupContext("close");
-  __Pyx_INCREF((PyObject *)__pyx_v_self);
-
-  /* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":27
- *             raise IOError( "Could not open file" )
- *     def close( self ):
- *         if self.bgzf:             # <<<<<<<<<<<<<<
- *             bgzf_close( self.bgzf )
- *     def read( self, int length ):
- */
-  __pyx_t_1 = (((struct __pyx_obj_2bx_4misc_4bgzf_BGZFFile *)__pyx_v_self)->bgzf != 0);
-  if (__pyx_t_1) {
-
-    /* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":28
- *     def close( self ):
- *         if self.bgzf:
- *             bgzf_close( self.bgzf )             # <<<<<<<<<<<<<<
- *     def read( self, int length ):
- *         cdef object rval = PyString_FromStringAndSize( NULL, length )
- */
-    bgzf_close(((struct __pyx_obj_2bx_4misc_4bgzf_BGZFFile *)__pyx_v_self)->bgzf);
-    goto __pyx_L5;
-  }
-  __pyx_L5:;
-
-  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
-  __Pyx_DECREF((PyObject *)__pyx_v_self);
-  __Pyx_XGIVEREF(__pyx_r);
-  __Pyx_RefNannyFinishContext();
-  return __pyx_r;
-}
-
-/* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":29
- *         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 )
- */
-
-static PyObject *__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_read(PyObject *__pyx_v_self, PyObject *__pyx_arg_length); /*proto*/
-static PyObject *__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_read(PyObject *__pyx_v_self, PyObject *__pyx_arg_length) {
-  int __pyx_v_length;
-  PyObject *__pyx_v_rval = 0;
-  PyObject *__pyx_r = NULL;
-  PyObject *__pyx_t_1 = NULL;
-  __Pyx_RefNannySetupContext("read");
-  assert(__pyx_arg_length); {
-    __pyx_v_length = __Pyx_PyInt_AsInt(__pyx_arg_length); if (unlikely((__pyx_v_length == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-  }
-  goto __pyx_L4_argument_unpacking_done;
-  __pyx_L3_error:;
-  __Pyx_AddTraceback("bx.misc.bgzf.BGZFFile.read");
-  return NULL;
-  __pyx_L4_argument_unpacking_done:;
-
-  /* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":30
- *             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
- */
-  __pyx_t_1 = PyString_FromStringAndSize(NULL, __pyx_v_length); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_1);
-  __pyx_v_rval = __pyx_t_1;
-  __pyx_t_1 = 0;
-
-  /* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":31
- *     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 ):
- */
-  bgzf_read(((struct __pyx_obj_2bx_4misc_4bgzf_BGZFFile *)__pyx_v_self)->bgzf, PyString_AsString(__pyx_v_rval), __pyx_v_length);
-
-  /* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":32
- *         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 )
- */
-  __Pyx_XDECREF(__pyx_r);
-  __Pyx_INCREF(__pyx_v_rval);
-  __pyx_r = __pyx_v_rval;
-  goto __pyx_L0;
-
-  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
-  goto __pyx_L0;
-  __pyx_L1_error:;
-  __Pyx_XDECREF(__pyx_t_1);
-  __Pyx_AddTraceback("bx.misc.bgzf.BGZFFile.read");
-  __pyx_r = NULL;
-  __pyx_L0:;
-  __Pyx_XDECREF(__pyx_v_rval);
-  __Pyx_XGIVEREF(__pyx_r);
-  __Pyx_RefNannyFinishContext();
-  return __pyx_r;
-}
-
-/* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":33
- *         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 ):
- */
-
-static PyObject *__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_tell(PyObject *__pyx_v_self, PyObject *unused); /*proto*/
-static PyObject *__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_tell(PyObject *__pyx_v_self, PyObject *unused) {
-  PyObject *__pyx_r = NULL;
-  PyObject *__pyx_t_1 = NULL;
-  __Pyx_RefNannySetupContext("tell");
-
-  /* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":34
- *         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 )
- */
-  __Pyx_XDECREF(__pyx_r);
-  __pyx_t_1 = PyLong_FromUnsignedLongLong(bgzf_tell(((struct __pyx_obj_2bx_4misc_4bgzf_BGZFFile *)__pyx_v_self)->bgzf)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_1);
-  __pyx_r = __pyx_t_1;
-  __pyx_t_1 = 0;
-  goto __pyx_L0;
-
-  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
-  goto __pyx_L0;
-  __pyx_L1_error:;
-  __Pyx_XDECREF(__pyx_t_1);
-  __Pyx_AddTraceback("bx.misc.bgzf.BGZFFile.tell");
-  __pyx_r = NULL;
-  __pyx_L0:;
-  __Pyx_XGIVEREF(__pyx_r);
-  __Pyx_RefNannyFinishContext();
-  return __pyx_r;
-}
-
-/* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":35
- *     def tell( self ):
- *         return bgzf_tell( self.bgzf )
- *     def seek( self, int64_t pos, int where=0 ):             # <<<<<<<<<<<<<<
- *         return bgzf_seek( self.bgzf, pos, where )
- */
-
-static PyObject *__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyObject *__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
-  __pyx_t_2bx_4misc_4bgzf_int64_t __pyx_v_pos;
-  int __pyx_v_where;
-  PyObject *__pyx_r = NULL;
-  PyObject *__pyx_t_1 = NULL;
-  static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__pos,&__pyx_n_s__where,0};
-  __Pyx_RefNannySetupContext("seek");
-  if (unlikely(__pyx_kwds)) {
-    Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
-    PyObject* values[2] = {0,0};
-    switch (PyTuple_GET_SIZE(__pyx_args)) {
-      case  2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
-      case  1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
-      case  0: break;
-      default: goto __pyx_L5_argtuple_error;
-    }
-    switch (PyTuple_GET_SIZE(__pyx_args)) {
-      case  0:
-      values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos);
-      if (likely(values[0])) kw_args--;
-      else goto __pyx_L5_argtuple_error;
-      case  1:
-      if (kw_args > 1) {
-        PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__where);
-        if (unlikely(value)) { values[1] = value; kw_args--; }
-      }
-    }
-    if (unlikely(kw_args > 0)) {
-      if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-    }
-    __pyx_v_pos = __Pyx_PyInt_AsUnsignedLongLong(values[0]); if (unlikely((__pyx_v_pos == (unsigned PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-    if (values[1]) {
-      __pyx_v_where = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_where == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-    } else {
-      __pyx_v_where = ((int)0);
-    }
-  } else {
-    __pyx_v_where = ((int)0);
-    switch (PyTuple_GET_SIZE(__pyx_args)) {
-      case  2: __pyx_v_where = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_where == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-      case  1: __pyx_v_pos = __Pyx_PyInt_AsUnsignedLongLong(PyTuple_GET_ITEM(__pyx_args, 0)); if (unlikely((__pyx_v_pos == (unsigned PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-      break;
-      default: goto __pyx_L5_argtuple_error;
-    }
-  }
-  goto __pyx_L4_argument_unpacking_done;
-  __pyx_L5_argtuple_error:;
-  __Pyx_RaiseArgtupleInvalid("seek", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-  __pyx_L3_error:;
-  __Pyx_AddTraceback("bx.misc.bgzf.BGZFFile.seek");
-  return NULL;
-  __pyx_L4_argument_unpacking_done:;
-
-  /* "/usr/local/src/bx-python/lib/bx/misc/bgzf.pyx":36
- *         return bgzf_tell( self.bgzf )
- *     def seek( self, int64_t pos, int where=0 ):
- *         return bgzf_seek( self.bgzf, pos, where )             # <<<<<<<<<<<<<<
- */
-  __Pyx_XDECREF(__pyx_r);
-  __pyx_t_1 = PyLong_FromUnsignedLongLong(bgzf_seek(((struct __pyx_obj_2bx_4misc_4bgzf_BGZFFile *)__pyx_v_self)->bgzf, __pyx_v_pos, __pyx_v_where)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_1);
-  __pyx_r = __pyx_t_1;
-  __pyx_t_1 = 0;
-  goto __pyx_L0;
-
-  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
-  goto __pyx_L0;
-  __pyx_L1_error:;
-  __Pyx_XDECREF(__pyx_t_1);
-  __Pyx_AddTraceback("bx.misc.bgzf.BGZFFile.seek");
-  __pyx_r = NULL;
-  __pyx_L0:;
-  __Pyx_XGIVEREF(__pyx_r);
-  __Pyx_RefNannyFinishContext();
-  return __pyx_r;
-}
-
-static PyObject *__pyx_tp_new_2bx_4misc_4bgzf_BGZFFile(PyTypeObject *t, PyObject *a, PyObject *k) {
-  PyObject *o = (*t->tp_alloc)(t, 0);
-  if (!o) return 0;
-  return o;
-}
-
-static void __pyx_tp_dealloc_2bx_4misc_4bgzf_BGZFFile(PyObject *o) {
-  (*Py_TYPE(o)->tp_free)(o);
-}
-
-static struct PyMethodDef __pyx_methods_2bx_4misc_4bgzf_BGZFFile[] = {
-  {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_close, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("read"), (PyCFunction)__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_read, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_tell, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_2bx_4misc_4bgzf_8BGZFFile_seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
-  {0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_BGZFFile = {
-  0, /*nb_add*/
-  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*/
-  0, /*nb_rshift*/
-  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, /*reserved*/
-  #else
-  0, /*nb_long*/
-  #endif
-  0, /*nb_float*/
-  #if PY_MAJOR_VERSION < 3
-  0, /*nb_oct*/
-  #endif
-  #if PY_MAJOR_VERSION < 3
-  0, /*nb_hex*/
-  #endif
-  0, /*nb_inplace_add*/
-  0, /*nb_inplace_subtract*/
-  0, /*nb_inplace_multiply*/
-  #if PY_MAJOR_VERSION < 3
-  0, /*nb_inplace_divide*/
-  #endif
-  0, /*nb_inplace_remainder*/
-  0, /*nb_inplace_power*/
-  0, /*nb_inplace_lshift*/
-  0, /*nb_inplace_rshift*/
-  0, /*nb_inplace_and*/
-  0, /*nb_inplace_xor*/
-  0, /*nb_inplace_or*/
-  0, /*nb_floor_divide*/
-  0, /*nb_true_divide*/
-  0, /*nb_inplace_floor_divide*/
-  0, /*nb_inplace_true_divide*/
-  #if (PY_MAJOR_VERSION >= 3) || (Py_TPFLAGS_DEFAULT & Py_TPFLAGS_HAVE_INDEX)
-  0, /*nb_index*/
-  #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_BGZFFile = {
-  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_BGZFFile = {
-  0, /*mp_length*/
-  0, /*mp_subscript*/
-  0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_BGZFFile = {
-  #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_2bx_4misc_4bgzf_BGZFFile = {
-  PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("bx.misc.bgzf.BGZFFile"), /*tp_name*/
-  sizeof(struct __pyx_obj_2bx_4misc_4bgzf_BGZFFile), /*tp_basicsize*/
-  0, /*tp_itemsize*/
-  __pyx_tp_dealloc_2bx_4misc_4bgzf_BGZFFile, /*tp_dealloc*/
-  0, /*tp_print*/
-  0, /*tp_getattr*/
-  0, /*tp_setattr*/
-  0, /*tp_compare*/
-  0, /*tp_repr*/
-  &__pyx_tp_as_number_BGZFFile, /*tp_as_number*/
-  &__pyx_tp_as_sequence_BGZFFile, /*tp_as_sequence*/
-  &__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 inteber strings
+        # Counting n-grams in integer 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;
-        }
-        status = deflateEnd(&zs);
-        if (status != Z_OK) {