diff srf2fastq/io_lib-1.12.2/io_lib/compress.h @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/compress.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,102 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _COMPRESS_H
+#define _COMPRESS_H
+
+#include <stdio.h>
+
+#include "io_lib/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Compress a file using the method set in the compression_used value
+ * (set by set_compression_method and fopen_compressed).
+ *
+ * If compression succeeds, we rename the file back its original name.
+ *
+ * When compression_used is 0 no compression is done.
+ */
+int compress_file(char *file);
+int fcompress_file(mFILE *fp);
+
+/*
+ * Returns a file pointer of an uncompressed copy of 'file'.
+ * 'file' need not exist if 'file'.ext (eg file.gz)
+ * exists and can be uncompressed.
+ *
+ * If ofp is non NULL then the original file pointer will also be returned
+ * (opened for update) to allow writing back to the original file. In cases
+ * of uncompressed data this is the same as the returned file pointer.
+ */
+mFILE *fopen_compressed(char *file, mFILE **ofp);
+
+/*
+ * Returns a file pointer of an uncompressed copy of 'fp'.
+ *
+ * If ofp is non NULL then the original file pointer will also be returned
+ * (opened for update) to allow writing back to the original file. In cases
+ * of uncompressed data this is the same as the returned file pointer.
+ */
+mFILE *freopen_compressed(mFILE *fp, mFILE **ofp);
+
+/*
+ * Sets the desired compression method. The below macros relate to entries
+ * in the compression magic numbers table.
+ */
+void set_compression_method(int method);
+int get_compression_method(void);
+
+/*
+ * Converts compress mode strings (eg "gzip") to numbers.
+ */
+int compress_str2int(char *mode);
+
+/*
+ * Converts compress mode numbers to strings (eg "gzip").
+ */
+char *compress_int2str(int mode);
+
+#define COMP_METHOD_NONE	0
+#define COMP_METHOD_BZIP	1
+#define COMP_METHOD_GZIP	2
+#define COMP_METHOD_COMPRESS	3
+#define COMP_METHOD_BZIP2	5
+#define COMP_METHOD_SZIP	6
+
+/*
+ * In memory gzip and gunzip using zlib. In each case data is the input
+ * data (with 'size') and the returned value is the output data along with
+ * [cu]data_size being the returned data size.
+ *
+ * Both return NULL on failure
+ */
+char *memgzip(char *data, size_t size, size_t *cdata_size);
+char *memgunzip(char *data, size_t size, size_t *udata_size);
+
+/*
+ * Given a filename remove a known compression extension
+ *
+ * Returns: None
+ */
+void remove_extension(char *file);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _COMPRESS_H */