--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/razf.h	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,134 @@
+ /*-
+ * RAZF : Random Access compressed(Z) File
+ * Version: 1.0
+ * Release Date: 2008-10-27
+ *
+ * Copyright 2008, Jue Ruan <ruanjue@gmail.com>, Heng Li <lh3@sanger.ac.uk>
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ */
+
+
+#ifndef __RAZF_RJ_H
+#define __RAZF_RJ_H
+
+#include <stdint.h>
+#include <stdio.h>
+#include "zlib.h"
+
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+#if ZLIB_VERNUM < 0x1221
+#define _RZ_READONLY
+struct _gz_header_s;
+typedef struct _gz_header_s _gz_header;
+#define gz_header _gz_header
+#endif
+
+#define WINDOW_BITS   15
+
+#ifndef RZ_BLOCK_SIZE
+#define RZ_BLOCK_SIZE (1<<WINDOW_BITS)
+#endif
+
+#ifndef RZ_BUFFER_SIZE
+#define RZ_BUFFER_SIZE 4096
+#endif
+
+#ifndef RZ_COMPRESS_LEVEL
+#define RZ_COMPRESS_LEVEL 6
+#endif
+
+#define RZ_BIN_SIZE ((1LLU << 32) / RZ_BLOCK_SIZE)
+
+typedef struct {
+	uint32_t *cell_offsets; // i
+	int64_t  *bin_offsets; // i / BIN_SIZE
+	int size;
+	int cap;
+} ZBlockIndex;
+/* When storing index, output bytes in Big-Endian everywhere */
+
+#define FILE_TYPE_RZ	1
+#define FILE_TYPE_PLAIN	2
+#define FILE_TYPE_GZ	3
+
+typedef struct RandomAccessZFile  {
+	char mode; /* 'w' : write mode; 'r' : read mode */
+	int file_type;
+	/* plain file or rz file, razf_read support plain file as input too, in this case, razf_read work as buffered fread */
+#ifdef _USE_KNETFILE
+    union {
+        knetFile *fpr;
+        int fpw;
+    } x;
+#else
+	int filedes; /* the file descriptor */
+#endif
+	z_stream *stream;
+	ZBlockIndex *index;
+	int64_t in, out, end, src_end;
+	/* in: n bytes total in; out: n bytes total out; */
+	/* end: the end of all data blocks, while the start of index; src_end: the true end position in uncompressed file */
+	int buf_flush; // buffer should be flush, suspend inflate util buffer is empty
+	int64_t block_pos, block_off, next_block_pos;
+	/* block_pos: the start postiion of current block  in compressed file */
+	/* block_off: tell how many bytes have been read from current block */
+	void *inbuf, *outbuf;
+	int header_size;
+	gz_header *header;
+	/* header is used to transfer inflate_state->mode from HEAD to TYPE after call inflateReset */
+	int buf_off, buf_len;
+	int z_err, z_eof;
+	int seekable;
+	/* Indice where the source is seekable */
+	int load_index;
+	/* set has_index to 0 in mode 'w', then index will be discarded */
+} RAZF;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	RAZF* razf_dopen(int data_fd, const char *mode);
+	RAZF *razf_open(const char *fn, const char *mode);
+	int razf_write(RAZF* rz, const void *data, int size);
+	int razf_read(RAZF* rz, void *data, int size);
+	int64_t razf_seek(RAZF* rz, int64_t pos, int where);
+	void razf_close(RAZF* rz);
+
+#define razf_tell(rz) ((rz)->out)
+
+	RAZF* razf_open2(const char *filename, const char *mode);
+	RAZF* razf_dopen2(int fd, const char *mode);
+	uint64_t razf_tell2(RAZF *rz);
+	int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif