libStatGen Software
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bgzf.h
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/* The MIT License
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Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
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2011 Attractive Chaos <attractor@live.co.uk>
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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*/
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/* The BGZF library was originally written by Bob Handsaker from the Broad
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* Institute. It was later improved by the SAMtools developers. */
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#ifndef __BGZF_H
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#define __BGZF_H
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#include <stdint.h>
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#include <stdio.h>
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#ifdef __ZLIB_AVAILABLE__
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#include <zlib.h>
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#endif
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#define BGZF_BLOCK_SIZE 0x10000
// 64k
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#define BGZF_ERR_ZLIB 1
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#define BGZF_ERR_HEADER 2
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#define BGZF_ERR_IO 4
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#define BGZF_ERR_MISUSE 8
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typedef
struct
{
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int
open_mode:8, compress_level:8, errcode:16;
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int
cache_size;
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int
block_length, block_offset;
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int64_t block_address;
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void
*uncompressed_block, *compressed_block;
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void
*cache;
// a pointer to a hash table
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void
*fp;
// actual file handler; FILE* on writing; FILE* or knetFile* on reading
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}
BGZF
;
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#ifndef KSTRING_T
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#define KSTRING_T kstring_t
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typedef
struct
__kstring_t
{
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size_t
l, m;
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char
*s;
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}
kstring_t
;
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#endif
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#ifdef __cplusplus
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extern
"C"
{
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#endif
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BGZF
* dummy();
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/******************
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* Basic routines *
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******************/
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/**
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* Open an existing file descriptor for reading or writing.
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*
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* @param fd file descriptor
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* @param mode mode matching /[rwu0-9]+/: 'r' for reading, 'w' for writing and a digit specifies
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* the zlib compression level; if both 'r' and 'w' are present, 'w' is ignored.
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* @return BGZF file handler; 0 on error
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*/
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BGZF
* bgzf_dopen(
int
fd,
const
char
*mode);
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/**
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* Open the specified file for reading or writing.
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*/
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BGZF
* bgzf_open(
const
char
* path,
const
char
*mode);
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/**
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* Close the BGZF and free all associated resources.
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*
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* @param fp BGZF file handler
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* @return 0 on success and -1 on error
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*/
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int
bgzf_close(
BGZF
*fp);
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/**
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* Read up to _length_ bytes from the file storing into _data_.
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*
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* @param fp BGZF file handler
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* @param data data array to read into
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* @param length size of data to read
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* @return number of bytes actually read; 0 on end-of-file and -1 on error
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*/
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ssize_t bgzf_read(
BGZF
*fp,
void
*data, ssize_t length);
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/**
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* Write _length_ bytes from _data_ to the file.
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*
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* @param fp BGZF file handler
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* @param data data array to write
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* @param length size of data to write
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* @return number of bytes actually written; -1 on error
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*/
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ssize_t bgzf_write(
BGZF
*fp,
const
void
*data, ssize_t length);
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/**
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* Write the data in the buffer to the file.
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*/
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int
bgzf_flush(
BGZF
*fp);
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/**
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* Return a virtual file pointer to the current location in the file.
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* No interpetation of the value should be made, other than a subsequent
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* call to bgzf_seek can be used to position the file at the same point.
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* Return value is non-negative on success.
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*/
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#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
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/**
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* Set the file to read from the location specified by _pos_.
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*
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* @param fp BGZF file handler
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* @param pos virtual file offset returned by bgzf_tell()
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* @param whence must be SEEK_SET
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* @return 0 on success and -1 on error
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*/
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int64_t bgzf_seek(
BGZF
*fp, int64_t pos,
int
whence);
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/**
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* Check if the BGZF end-of-file (EOF) marker is present
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*
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* @param fp BGZF file handler opened for reading
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* @return 1 if EOF is present; 0 if not or on I/O error
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*/
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int
bgzf_check_EOF(
BGZF
*fp);
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/**
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* Check if a file is in the BGZF format
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*
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* @param fn file name
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* @return 1 if _fn_ is BGZF; 0 if not or on I/O error
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*/
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int
bgzf_is_bgzf(
const
char
*fn);
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/*********************
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* Advanced routines *
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*********************/
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/**
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* Set the cache size. Only effective when compiled with -DBGZF_CACHE.
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*
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* @param fp BGZF file handler
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* @param size size of cache in bytes; 0 to disable caching (default)
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*/
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void
bgzf_set_cache_size(
BGZF
*fp,
int
size);
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/**
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* Flush the file if the remaining buffer size is smaller than _size_
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*/
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int
bgzf_flush_try(
BGZF
*fp, ssize_t size);
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/**
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* Read one byte from a BGZF file. It is faster than bgzf_read()
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* @param fp BGZF file handler
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* @return byte read; -1 on end-of-file or error
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*/
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int
bgzf_getc(
BGZF
*fp);
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/**
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* Read one line from a BGZF file. It is faster than bgzf_getc()
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*
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* @param fp BGZF file handler
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* @param delim delimitor
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* @param str string to write to; must be initialized
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* @return length of the string; 0 on end-of-file; negative on error
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*/
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int
bgzf_getline(
BGZF
*fp,
int
delim,
kstring_t
*str);
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/**
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* Read the next BGZF block.
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*/
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int
bgzf_read_block(
BGZF
*fp);
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#ifdef __cplusplus
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}
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#endif
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#endif
BGZF
Definition
bgzf.h:44
__kstring_t
Definition
bgzf.h:56
samtools
bgzf.h
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