jpayne@69: # cython: language_level=3
jpayne@69: """Functions that read and write block gzipped files.
jpayne@69: 
jpayne@69: The user of the file doesn't have to worry about the compression
jpayne@69: and random access is allowed if an index file is present."""
jpayne@69: 
jpayne@69: # based on Python 3.5's gzip module
jpayne@69: 
jpayne@69: import io
jpayne@69: 
jpayne@69: from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
jpayne@69: from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
jpayne@69: from libc.stdio  cimport SEEK_SET
jpayne@69: from libc.stdlib cimport malloc, calloc, realloc, free
jpayne@69: 
jpayne@69: from cpython.object cimport PyObject
jpayne@69: from cpython.bytes  cimport PyBytes_FromStringAndSize, _PyBytes_Resize
jpayne@69: 
jpayne@69: from pysam.libcutils   cimport force_bytes, encode_filename
jpayne@69: from pysam.libchtslib  cimport bgzf_open, bgzf_index_build_init, bgzf_write, bgzf_read, \
jpayne@69:                                bgzf_flush, bgzf_index_dump, bgzf_close, bgzf_seek, \
jpayne@69:                                bgzf_tell, bgzf_getline, kstring_t, BGZF
jpayne@69: 
jpayne@69: __all__ = ["BGZFile"]
jpayne@69: 
jpayne@69: 
jpayne@69: BUFFER_SIZE = io.DEFAULT_BUFFER_SIZE
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class BGZFile(object):
jpayne@69:     """The BGZFile class simulates most of the methods of a file object with
jpayne@69:     the exception of the truncate() method.
jpayne@69: 
jpayne@69:     This class only supports opening files in binary mode. If you need to open a
jpayne@69:     compressed file in text mode, use the gzip.open() function.
jpayne@69:     """
jpayne@69:     def __init__(self, filename, mode=None, index=None):
jpayne@69:         """Constructor for the BGZFile class.
jpayne@69: 
jpayne@69:         The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', 'wb', 'x', or
jpayne@69:         'xb' depending on whether the file will be read or written.  The default
jpayne@69:         is the mode of fileobj if discernible; otherwise, the default is 'rb'.
jpayne@69:         A mode of 'r' is equivalent to one of 'rb', and similarly for 'w' and
jpayne@69:         'wb', 'a' and 'ab', and 'x' and 'xb'.
jpayne@69:         """
jpayne@69:         if mode and ('t' in mode or 'U' in mode):
jpayne@69:             raise ValueError("Invalid mode: {!r}".format(mode))
jpayne@69:         if not mode:
jpayne@69:             mode = 'rb'
jpayne@69:         elif mode and 'b' not in mode:
jpayne@69:             mode += 'b'
jpayne@69: 
jpayne@69:         mode = force_bytes(mode)
jpayne@69: 
jpayne@69:         self.name = encode_filename(filename)
jpayne@69:         self.index = encode_filename(index) if index is not None else None
jpayne@69: 
jpayne@69:         self.bgzf = bgzf_open(self.name, mode)
jpayne@69: 
jpayne@69:         if self.bgzf.is_write and index is not None and bgzf_index_build_init(self.bgzf) < 0:
jpayne@69:             raise IOError('Error building bgzf index')
jpayne@69: 
jpayne@69:     def __dealloc__(self):
jpayne@69:         self.close()
jpayne@69: 
jpayne@69:     def write(self, data):
jpayne@69:         if not self.bgzf:
jpayne@69:             raise ValueError("write() on closed BGZFile object")
jpayne@69: 
jpayne@69:         if not self.bgzf.is_write:
jpayne@69:             import errno
jpayne@69:             raise IOError(errno.EBADF, "write() on read-only BGZFile object")
jpayne@69: 
jpayne@69:         if isinstance(data, bytes):
jpayne@69:             length = len(data)
jpayne@69:         else:
jpayne@69:             # accept any data that supports the buffer protocol
jpayne@69:             data = memoryview(data)
jpayne@69:             length = data.nbytes
jpayne@69: 
jpayne@69:         if length > 0 and bgzf_write(self.bgzf, <char *>data, length) < 0:
jpayne@69:             raise IOError('BGZFile write failed')
jpayne@69: 
jpayne@69:         return length
jpayne@69: 
jpayne@69:     def read(self, size=-1):
jpayne@69:         cdef ssize_t read_size
jpayne@69: 
jpayne@69:         if not self.bgzf:
jpayne@69:             raise ValueError("read() on closed BGZFile object")
jpayne@69: 
jpayne@69:         if self.bgzf.is_write:
jpayne@69:             import errno
jpayne@69:             raise IOError(errno.EBADF, "read() on write-only BGZFile object")
jpayne@69: 
jpayne@69:         if size < 0:
jpayne@69:             chunks = []
jpayne@69:             while 1:
jpayne@69:                 chunk = PyBytes_FromStringAndSize(NULL, BUFFER_SIZE)
jpayne@69:                 cdata = <bytes>chunk
jpayne@69:                 read_size = bgzf_read(self.bgzf, <char *>chunk, BUFFER_SIZE)
jpayne@69:                 if read_size < 0:
jpayne@69:                     raise IOError('Error reading from BGZFile')
jpayne@69:                 elif not read_size:
jpayne@69:                     break
jpayne@69:                 elif read_size < BUFFER_SIZE:
jpayne@69:                     chunk = chunk[:read_size]
jpayne@69:                 chunks.append(chunk)
jpayne@69:             return b''.join(chunks)
jpayne@69: 
jpayne@69:         elif size > 0:
jpayne@69:             chunk = PyBytes_FromStringAndSize(NULL, size)
jpayne@69:             read_size = bgzf_read(self.bgzf, <char *>chunk, size)
jpayne@69:             if read_size < 0:
jpayne@69:                 raise IOError('Error reading from BGZFile')
jpayne@69:             elif read_size < size:
jpayne@69:                 chunk = chunk[:read_size]
jpayne@69:             return chunk
jpayne@69:         else:
jpayne@69:             return b''
jpayne@69: 
jpayne@69:     @property
jpayne@69:     def closed(self):
jpayne@69:         return self.bgzf == NULL
jpayne@69: 
jpayne@69:     def close(self):
jpayne@69:         if not self.bgzf:
jpayne@69:             return
jpayne@69: 
jpayne@69:         if self.bgzf.is_write and bgzf_flush(self.bgzf) < 0:
jpayne@69:             raise IOError('Error flushing BGZFile object')
jpayne@69: 
jpayne@69:         if self.index and bgzf_index_dump(self.bgzf, self.index, NULL) < 0:
jpayne@69:             raise IOError('Cannot write index')
jpayne@69: 
jpayne@69:         cdef ret = bgzf_close(self.bgzf)
jpayne@69:         self.bgzf = NULL
jpayne@69: 
jpayne@69:         if ret < 0:
jpayne@69:             raise IOError('Error closing BGZFile object')
jpayne@69: 
jpayne@69:     def __enter__(self):
jpayne@69:         return self
jpayne@69: 
jpayne@69:     def __exit__(self, type, value, tb):
jpayne@69:         self.close()
jpayne@69: 
jpayne@69:     def flush(self):
jpayne@69:         if not self.bgzf:
jpayne@69:             return
jpayne@69: 
jpayne@69:         if self.bgzf.is_write and bgzf_flush(self.bgzf) < 0:
jpayne@69:             raise IOError('Error flushing BGZFile object')
jpayne@69: 
jpayne@69:     def fileno(self):
jpayne@69:         """Invoke the underlying file object's fileno() method.
jpayne@69: 
jpayne@69:         This will raise AttributeError if the underlying file object
jpayne@69:         doesn't support fileno().
jpayne@69:         """
jpayne@69:         raise AttributeError('fileno')
jpayne@69: 
jpayne@69:     def rewind(self):
jpayne@69:         '''Return the uncompressed stream file position indicator to the
jpayne@69:         beginning of the file'''
jpayne@69:         if not self.bgzf:
jpayne@69:             raise ValueError("rewind() on closed BGZFile object")
jpayne@69:         if not self.bgzf.is_write:
jpayne@69:             raise IOError("Can't rewind in write mode")
jpayne@69:         if bgzf_seek(self.bgzf, 0, SEEK_SET) < 0:
jpayne@69:             raise IOError('Error seeking BGZFFile object')
jpayne@69: 
jpayne@69:     def readable(self):
jpayne@69:         if not self.bgzf:
jpayne@69:             raise ValueError("readable() on closed BGZFile object")
jpayne@69:         return self.bgzf != NULL and not self.bgzf.is_write
jpayne@69: 
jpayne@69:     def writable(self):
jpayne@69:         return self.bgzf != NULL and self.bgzf.is_write
jpayne@69: 
jpayne@69:     def seekable(self):
jpayne@69:         return True
jpayne@69: 
jpayne@69:     def tell(self):
jpayne@69:         if not self.bgzf:
jpayne@69:             raise ValueError("seek() on closed BGZFile object")
jpayne@69:         cdef int64_t off = bgzf_tell(self.bgzf)
jpayne@69:         if off < 0:
jpayne@69:             raise IOError('Error in tell on BGZFFile object')
jpayne@69: 
jpayne@69:         return off
jpayne@69: 
jpayne@69:     def seek(self, offset, whence=io.SEEK_SET):
jpayne@69:         if not self.bgzf:
jpayne@69:             raise ValueError("seek() on closed BGZFile object")
jpayne@69:         if whence is not io.SEEK_SET:
jpayne@69:             raise ValueError('Seek from end not supported')
jpayne@69: 
jpayne@69:         cdef int64_t off = bgzf_seek(self.bgzf, offset, SEEK_SET)
jpayne@69:         if off < 0:
jpayne@69:             raise IOError('Error seeking BGZFFile object')
jpayne@69: 
jpayne@69:         return off
jpayne@69: 
jpayne@69:     def readline(self, size=-1):
jpayne@69:         if not self.bgzf:
jpayne@69:             raise ValueError("readline() on closed BGZFile object")
jpayne@69: 
jpayne@69:         cdef kstring_t line
jpayne@69:         cdef char c
jpayne@69: 
jpayne@69:         line.l = line.m = 0
jpayne@69:         line.s = NULL
jpayne@69: 
jpayne@69:         cdef int ret = bgzf_getline(self.bgzf, b'\n', &line)
jpayne@69:         if ret == -1:
jpayne@69:             s = b''
jpayne@69:         elif ret == -2:
jpayne@69:             if line.m:
jpayne@69:                 free(line.s)
jpayne@69:             raise IOError('Error reading line in BGZFFile object')
jpayne@69:         else:
jpayne@69:             s = line.s[:line.l]
jpayne@69: 
jpayne@69:         if line.m:
jpayne@69:             free(line.s)
jpayne@69: 
jpayne@69:         return s
jpayne@69: 
jpayne@69:     def __iter__(self):
jpayne@69:         return self
jpayne@69: 
jpayne@69:     def __next__(self):
jpayne@69:         line = self.readline()
jpayne@69:         if not line:
jpayne@69:             raise StopIteration()
jpayne@69:         return line