Merge commit 'upstream/0.3'

[pysam.git] / tabix / bgzf.h

diff --git a/tabix/bgzf.h b/tabix/bgzf.h
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+++ b/tabix/bgzf.h
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+/* 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.
+*/
+
+#ifndef __BGZF_H
+#define __BGZF_H
+
+#include <stdint.h>
+#include <stdio.h>
+#include <stdbool.h>
+#include <zlib.h>
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+//typedef int8_t bool;
+
+typedef struct {
+    int file_descriptor;
+    char open_mode;  // 'r' or 'w'
+    bool owned_file, is_uncompressed;
+#ifdef _USE_KNETFILE
+       union {
+               knetFile *fpr;
+               FILE *fpw;
+       } x;
+#else
+    FILE* file;
+#endif
+    int uncompressed_block_size;
+    int compressed_block_size;
+    void* uncompressed_block;
+    void* compressed_block;
+    int64_t block_address;
+    int block_length;
+    int block_offset;
+       int cache_size;
+    const char* error;
+       void *cache; // a pointer to a hash table
+} BGZF;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Open an existing file descriptor for reading or writing.
+ * Mode must be either "r" or "w".
+ * A subsequent bgzf_close will not close the file descriptor.
+ * Returns null on error.
+ */
+BGZF* bgzf_fdopen(int fd, const char* __restrict mode);
+
+/*
+ * Open the specified file for reading or writing.
+ * Mode must be either "r" or "w".
+ * Returns null on error.
+ */
+BGZF* bgzf_open(const char* path, const char* __restrict mode);
+
+/*
+ * Close the BGZ file and free all associated resources.
+ * Does not close the underlying file descriptor if created with bgzf_fdopen.
+ * Returns zero on success, -1 on error.
+ */
+int bgzf_close(BGZF* fp);
+
+/*
+ * Read up to length bytes from the file storing into data.
+ * Returns the number of bytes actually read.
+ * Returns zero on end of file.
+ * Returns -1 on error.
+ */
+int bgzf_read(BGZF* fp, void* data, int length);
+
+/*
+ * Write length bytes from data to the file.
+ * Returns the number of bytes written.
+ * Returns -1 on error.
+ */
+int bgzf_write(BGZF* fp, const void* data, int length);
+
+/*
+ * 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.
+ * Returns -1 on error.
+ */
+#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
+
+/*
+ * Set the file to read from the location specified by pos, which must
+ * be a value previously returned by bgzf_tell for this file (but not
+ * necessarily one returned by this file handle).
+ * The where argument must be SEEK_SET.
+ * Seeking on a file opened for write is not supported.
+ * Returns zero on success, -1 on error.
+ */
+int64_t bgzf_seek(BGZF* fp, int64_t pos, int where);
+
+/*
+ * Set the cache size. Zero to disable. By default, caching is
+ * disabled. The recommended cache size for frequent random access is
+ * about 8M bytes.
+ */
+void bgzf_set_cache_size(BGZF *fp, int cache_size);
+
+int bgzf_check_EOF(BGZF *fp);
+
+int bgzf_read_block(BGZF* fp);
+
+#ifdef __cplusplus
+}
+#endif
+
+static inline int bgzf_getc(BGZF *fp)
+{
+       int c;
+       if (fp->block_offset >= fp->block_length) {
+               if (bgzf_read_block(fp) != 0) return -2; /* error */
+               if (fp->block_length == 0) return -1; /* end-of-file */
+       }
+       c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
+    if (fp->block_offset == fp->block_length) {
+#ifdef _USE_KNETFILE
+        fp->block_address = knet_tell(fp->x.fpr);
+#else
+        fp->block_address = ftello(fp->file);
+#endif
+        fp->block_offset = 0;
+        fp->block_length = 0;
+    }
+       return c;
+}
+
+#endif