diff bwa-0.6.2/utils.h @ 2:a294fbfcb1db draft default tip

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/utils.h	Fri Jul 18 07:55:59 2014 -0400
@@ -0,0 +1,73 @@
+/* The MIT License
+
+   Copyright (c) 2008 Genome Research Ltd (GRL).
+
+   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.
+*/
+
+/* Contact: Heng Li <[e-mail]> */
+
+#ifndef LH3_UTILS_H
+#define LH3_UTILS_H
+
+#include <stdio.h>
+#include <zlib.h>
+
+#ifdef __GNUC__
+// Tell GCC to validate printf format string and args
+#define ATTRIBUTE(list) __attribute__ (list)
+#else
+#define ATTRIBUTE(list)
+#endif
+
+
+
+#define err_fatal_simple(msg) err_fatal_simple_core(__func__, msg)
+#define xopen(fn, mode) err_xopen_core(__func__, fn, mode)
+#define xreopen(fn, mode, fp) err_xreopen_core(__func__, fn, mode, fp)
+#define xzopen(fn, mode) err_xzopen_core(__func__, fn, mode)
+#define xassert(cond, msg) if ((cond) == 0) err_fatal_simple_core(__func__, msg)
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	void err_fatal(const char *header, const char *fmt, ...);
+	void err_fatal_simple_core(const char *func, const char *msg);
+	FILE *err_xopen_core(const char *func, const char *fn, const char *mode);
+	FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp);
+	gzFile err_xzopen_core(const char *func, const char *fn, const char *mode);
+    size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream);
+	int err_fprintf(FILE *stream, const char *format, ...)
+        ATTRIBUTE((format(printf, 2, 3)));
+	int err_printf(const char *format, ...)
+        ATTRIBUTE((format(printf, 1, 2)));
+	int err_fflush(FILE *stream);
+	int err_fclose(FILE *stream);
+
+	double cputime();
+	double realtime();
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif