diff PsiCLASS-1.0.2/samtools-0.1.19/bgzf.h @ 0:903fc43d6227 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/bgzf.h	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,207 @@
+/* The MIT License
+
+   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+                 2011, 2012 Attractive Chaos <[e-mail]>
+
+   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.
+*/
+
+/* The BGZF library was originally written by Bob Handsaker from the Broad
+ * Institute. It was later improved by the SAMtools developers. */
+
+#ifndef __BGZF_H
+#define __BGZF_H
+
+#include <stdint.h>
+#include <stdio.h>
+#include <zlib.h>
+#include <sys/types.h>
+
+#define BGZF_BLOCK_SIZE     0xff00 // make sure compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE
+#define BGZF_MAX_BLOCK_SIZE 0x10000
+
+#define BGZF_ERR_ZLIB   1
+#define BGZF_ERR_HEADER 2
+#define BGZF_ERR_IO     4
+#define BGZF_ERR_MISUSE 8
+
+typedef struct {
+	int errcode:16, is_write:2, compress_level:14;
+	int cache_size;
+    int block_length, block_offset;
+    int64_t block_address;
+    void *uncompressed_block, *compressed_block;
+	void *cache; // a pointer to a hash table
+	void *fp; // actual file handler; FILE* on writing; FILE* or knetFile* on reading
+	void *mt; // only used for multi-threading
+} BGZF;
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+	size_t l, m;
+	char *s;
+} kstring_t;
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	/******************
+	 * Basic routines *
+	 ******************/
+
+	/**
+	 * Open an existing file descriptor for reading or writing.
+	 *
+	 * @param fd    file descriptor
+	 * @param mode  mode matching /[rwu0-9]+/: 'r' for reading, 'w' for writing and a digit specifies
+	 *              the zlib compression level; if both 'r' and 'w' are present, 'w' is ignored.
+	 * @return      BGZF file handler; 0 on error
+	 */
+	BGZF* bgzf_dopen(int fd, const char *mode);
+
+	#define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility
+
+	/**
+	 * Open the specified file for reading or writing.
+	 */
+	BGZF* bgzf_open(const char* path, const char *mode);
+
+	/**
+	 * Close the BGZF and free all associated resources.
+	 *
+	 * @param fp    BGZF file handler
+	 * @return      0 on success and -1 on error
+	 */
+	int bgzf_close(BGZF *fp);
+
+	/**
+	 * Read up to _length_ bytes from the file storing into _data_.
+	 *
+	 * @param fp     BGZF file handler
+	 * @param data   data array to read into
+	 * @param length size of data to read
+	 * @return       number of bytes actually read; 0 on end-of-file and -1 on error
+	 */
+	ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length);
+
+	/**
+	 * Write _length_ bytes from _data_ to the file.
+	 *
+	 * @param fp     BGZF file handler
+	 * @param data   data array to write
+	 * @param length size of data to write
+	 * @return       number of bytes actually written; -1 on error
+	 */
+	ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length);
+
+	/**
+	 * Write the data in the buffer to the file.
+	 */
+	int bgzf_flush(BGZF *fp);
+
+	/**
+	 * Return a virtual file pointer to the current location in the file.
+	 * No interpetation of the value should be made, other than a subsequent
+	 * call to bgzf_seek can be used to position the file at the same point.
+	 * Return value is non-negative on success.
+	 */
+	#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
+
+	/**
+	 * Set the file to read from the location specified by _pos_.
+	 *
+	 * @param fp     BGZF file handler
+	 * @param pos    virtual file offset returned by bgzf_tell()
+	 * @param whence must be SEEK_SET
+	 * @return       0 on success and -1 on error
+	 */
+	int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence);
+
+	/**
+	 * Check if the BGZF end-of-file (EOF) marker is present
+	 *
+	 * @param fp    BGZF file handler opened for reading
+	 * @return      1 if EOF is present; 0 if not or on I/O error
+	 */
+	int bgzf_check_EOF(BGZF *fp);
+
+	/**
+	 * Check if a file is in the BGZF format
+	 *
+	 * @param fn    file name
+	 * @return      1 if _fn_ is BGZF; 0 if not or on I/O error
+	 */
+	 int bgzf_is_bgzf(const char *fn);
+
+	/*********************
+	 * Advanced routines *
+	 *********************/
+
+	/**
+	 * Set the cache size. Only effective when compiled with -DBGZF_CACHE.
+	 *
+	 * @param fp    BGZF file handler
+	 * @param size  size of cache in bytes; 0 to disable caching (default)
+	 */
+	void bgzf_set_cache_size(BGZF *fp, int size);
+
+	/**
+	 * Flush the file if the remaining buffer size is smaller than _size_ 
+	 */
+	int bgzf_flush_try(BGZF *fp, ssize_t size);
+
+	/**
+	 * Read one byte from a BGZF file. It is faster than bgzf_read()
+	 * @param fp     BGZF file handler
+	 * @return       byte read; -1 on end-of-file or error
+	 */
+	int bgzf_getc(BGZF *fp);
+
+	/**
+	 * Read one line from a BGZF file. It is faster than bgzf_getc()
+	 *
+	 * @param fp     BGZF file handler
+	 * @param delim  delimitor
+	 * @param str    string to write to; must be initialized
+	 * @return       length of the string; 0 on end-of-file; negative on error
+	 */
+	int bgzf_getline(BGZF *fp, int delim, kstring_t *str);
+
+	/**
+	 * Read the next BGZF block.
+	 */
+	int bgzf_read_block(BGZF *fp);
+
+	/**
+	 * Enable multi-threading (only effective on writing)
+	 *
+	 * @param fp          BGZF file handler; must be opened for writing
+	 * @param n_threads   #threads used for writing
+	 * @param n_sub_blks  #blocks processed by each thread; a value 64-256 is recommended
+	 */
+	int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif