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

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/utils.c	Fri Jul 18 07:55:59 2014 -0400
@@ -0,0 +1,164 @@
+/* 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]> */
+
+#include <stdio.h>
+#include <stdarg.h>
+#include <stdlib.h>
+#include <string.h>
+#include <zlib.h>
+#include <errno.h>
+#include <sys/resource.h>
+#include <sys/time.h>
+#include "utils.h"
+
+FILE *err_xopen_core(const char *func, const char *fn, const char *mode)
+{
+	FILE *fp = 0;
+	if (strcmp(fn, "-") == 0)
+		return (strstr(mode, "r"))? stdin : stdout;
+	if ((fp = fopen(fn, mode)) == 0) {
+		fprintf(stderr, "[%s] fail to open file '%s'. Abort!\n", func, fn);
+		abort();
+	}
+	return fp;
+}
+FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp)
+{
+	if (freopen(fn, mode, fp) == 0) {
+		fprintf(stderr, "[%s] fail to open file '%s': ", func, fn);
+		perror(NULL);
+		fprintf(stderr, "Abort!\n");
+		abort();
+	}
+	return fp;
+}
+gzFile err_xzopen_core(const char *func, const char *fn, const char *mode)
+{
+	gzFile fp;
+	if (strcmp(fn, "-") == 0)
+		return gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode);
+	if ((fp = gzopen(fn, mode)) == 0) {
+		fprintf(stderr, "[%s] fail to open file '%s'. Abort!\n", func, fn);
+		abort();
+	}
+	return fp;
+}
+void err_fatal(const char *header, const char *fmt, ...)
+{
+	va_list args;
+	va_start(args, fmt);
+	fprintf(stderr, "[%s] ", header);
+	vfprintf(stderr, fmt, args);
+	fprintf(stderr, " Abort!\n");
+	va_end(args);
+	abort();
+}
+
+void err_fatal_simple_core(const char *func, const char *msg)
+{
+	fprintf(stderr, "[%s] %s Abort!\n", func, msg);
+	abort();
+}
+
+size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream)
+{
+    size_t ret = fwrite(ptr, size, nmemb, stream);
+    if (ret != nmemb) 
+    {
+        err_fatal_simple_core("fwrite", strerror(errno));
+    }
+    return ret;
+}
+
+int err_printf(const char *format, ...) 
+{
+    va_list arg;
+    int done;
+
+    va_start(arg, format);
+    done = vfprintf(stdout, format, arg);
+    int saveErrno = errno;
+    va_end(arg);
+
+    if (done < 0) 
+    {
+        err_fatal_simple_core("vfprintf(stdout)", strerror(saveErrno));
+    }
+    return done;
+}
+
+int err_fprintf(FILE *stream, const char *format, ...) 
+{
+    va_list arg;
+    int done;
+
+    va_start(arg, format);
+    done = vfprintf(stream, format, arg);
+    int saveErrno = errno;
+    va_end(arg);
+
+    if (done < 0) 
+    {
+        err_fatal_simple_core("vfprintf", strerror(saveErrno));
+    }
+    return done;
+}
+
+int err_fflush(FILE *stream) 
+{
+    int ret = fflush(stream);
+    if (ret != 0) 
+    {
+        err_fatal_simple_core("fflush", strerror(errno));
+    }
+    return ret;
+}
+
+int err_fclose(FILE *stream) 
+{
+    int ret = fclose(stream);
+    if (ret != 0) 
+    {
+        err_fatal_simple_core("fclose", strerror(errno));
+    }
+    return ret;
+}
+
+double cputime()
+{
+	struct rusage r;
+	getrusage(RUSAGE_SELF, &r);
+	return r.ru_utime.tv_sec + r.ru_stime.tv_sec + 1e-6 * (r.ru_utime.tv_usec + r.ru_stime.tv_usec);
+}
+
+double realtime()
+{
+	struct timeval tp;
+	struct timezone tzp;
+	gettimeofday(&tp, &tzp);
+	return tp.tv_sec + tp.tv_usec * 1e-6;
+}