ONT source code changes to compile with MSVC 14

.gitignore

@@ -1,3 +1,5 @@
+.cproject
+.project
 .*.swp
 *.a
 *.o

gettimeofday.h

@@ -0,0 +1,71 @@
+#ifdef WIN32
+#ifndef _GETTIMEOFDAY_H
+#define _GETTIMEOFDAY_H
+
+#include <windows.h>
+
+struct timezone
+{
+  __int32  tz_minuteswest; /* minutes W of Greenwich */
+  int  tz_dsttime;     /* type of dst correction */
+};
+
+/*
+ * gettimeofday.c
+ *    Win32 gettimeofday() replacement
+ *    taken from PostgreSQL, according to
+ *    https://stackoverflow.com/questions/1676036/what-should-i-use-to-replace-gettimeofday-on-windows
+ *
+ * src/port/gettimeofday.c
+ *
+ * Copyright (c) 2003 SRA, Inc.
+ * Copyright (c) 2003 SKC, Inc.
+ *
+ * Permission to use, copy, modify, and distribute this software and
+ * its documentation for any purpose, without fee, and without a
+ * written agreement is hereby granted, provided that the above
+ * copyright notice and this paragraph and the following two
+ * paragraphs appear in all copies.
+ *
+ * IN NO EVENT SHALL THE AUTHOR BE LIABLE TO ANY PARTY FOR DIRECT,
+ * INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
+ * LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS
+ * DOCUMENTATION, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED
+ * OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * THE AUTHOR SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE.  THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS
+ * IS" BASIS, AND THE AUTHOR HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE,
+ * SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+ */
+
+/* FILETIME of Jan 1 1970 00:00:00. */
+static const unsigned __int64 epoch = ((unsigned __int64) 116444736000000000ULL);
+
+/*
+ * timezone information is stored outside the kernel so tzp isn't used anymore.
+ *
+ * Note: this function is not for Win32 high precision timing purpose. See
+ * elapsed_time().
+ */
+int
+gettimeofday(struct timeval * tp, struct timezone * tzp)
+{
+    FILETIME    file_time;
+    SYSTEMTIME  system_time;
+    ULARGE_INTEGER ularge;
+
+    GetSystemTime(&system_time);
+    SystemTimeToFileTime(&system_time, &file_time);
+    ularge.LowPart = file_time.dwLowDateTime;
+    ularge.HighPart = file_time.dwHighDateTime;
+
+    tp->tv_sec = (long) ((ularge.QuadPart - epoch) / 10000000L);
+    tp->tv_usec = (long) (system_time.wMilliseconds * 1000);
+
+    return 0;
+}
+
+#endif /* _GETTIMEOFDAY_H */
+#endif /* WIN32 */

index.c

@@ -1,6 +1,10 @@
 #include <stdlib.h>
 #include <assert.h>
+#ifdef WIN32
+#include <io.h>
+#else
 #include <unistd.h>
+#endif
 #include <fcntl.h>
 #include <stdio.h>
 #include "kthread.h"

kthread.c

@@ -1,6 +1,13 @@
 #include <pthread.h>
 #include <stdlib.h>
 #include <limits.h>
+#include <stdint.h>
+
+#ifdef WIN32
+#include <malloc.h>
+#define alloca _alloca
+#define __sync_fetch_and_add(ptr, addend)     _InterlockedExchangeAdd((void*)ptr, addend)
+#endif
 
 /************
  * kt_for() *

main.c

@@ -2,8 +2,12 @@
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
+#ifdef WIN32
+#include <time.h>
+#else
 #include <sys/resource.h>
 #include <sys/time.h>
+#endif
 #include "bseq.h"
 #include "minimap.h"
 #include "mmpriv.h"

misc.c

@@ -1,17 +1,40 @@
-#include <sys/resource.h>
-#include <sys/time.h>
-#include "minimap.h"
-
 int mm_verbose = 3;
 int mm_dbg_flag = 0;
 double mm_realtime0;
 
+#include "minimap.h"
+
+#ifdef WIN32
+#include "gettimeofday.h"
+
+// taken from https://stackoverflow.com/questions/5272470/c-get-cpu-usage-on-linux-and-windows
+#include <windows.h>
+double cputime() {
+  HANDLE hProcess = GetCurrentProcess();
+  FILETIME ftCreation, ftExit, ftKernel, ftUser;
+  SYSTEMTIME stKernel;
+  SYSTEMTIME stUser;
+
+  GetProcessTimes(hProcess, &ftCreation, &ftExit, &ftKernel, &ftUser);
+  FileTimeToSystemTime(&ftKernel, &stKernel);
+  FileTimeToSystemTime(&ftUser, &stUser);
+
+  double kernelModeTime = ((stKernel.wHour * 60.) + stKernel.wMinute * 60.) + stKernel.wSecond * 1. + stKernel.wMilliseconds / 1000.;
+  double userModeTime = ((stUser.wHour * 60.) + stUser.wMinute * 60.) + stUser.wSecond * 1. + stUser.wMilliseconds / 1000.;
+
+  return kernelModeTime + userModeTime;
+}
+#else
+#include <sys/resource.h>
+#include <sys/time.h>
+
 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);
 }
+#endif /* WIN32 */
 
 double realtime()
 {

sketch.c

@@ -5,6 +5,11 @@
 #include "kvec.h"
 #include "minimap.h"
 
+#ifdef WIN32
+#include <malloc.h>
+#define alloca _alloca
+#endif
+
 unsigned char seq_nt4_table[256] = {
 	0, 1, 2, 3,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,