From 0a3ebdc916de8e2e99e76d1438f2611534a3334c Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 2 Sep 2017 17:52:33 -0400
Subject: [PATCH] for better windows compatibility

---
 Makefile  |  7 ++++---
 index.c   |  4 ++--
 kthread.c |  2 +-
 main.c    | 14 ++++++--------
 misc.c    |  2 +-
 sdust.c   |  2 +-
 sketch.c  |  2 +-
 7 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/Makefile b/Makefile
index d1ed2c0..6ed7bae 100644
--- a/Makefile
+++ b/Makefile
@@ -30,8 +30,8 @@ minimap2-lite:example.o libminimap2.a
 libminimap2.a:$(OBJS)
 		$(AR) -csru $@ $(OBJS)
 
-sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h sdust.h
-		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
+sdust:sdust.c getopt.o kalloc.o kalloc.h kdq.h kvec.h kseq.h sdust.h
+		$(CC) -D_SDUST_MAIN $(CFLAGS) $< getopt.o kalloc.o -o $@ -lz
 
 clean:
 		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM session*
@@ -46,6 +46,7 @@ bseq.o: bseq.h kseq.h
 chain.o: minimap.h mmpriv.h bseq.h kalloc.h
 example.o: minimap.h kseq.h
 format.o: kalloc.h mmpriv.h minimap.h bseq.h
+getopt.o: getopt.h
 hit.o: mmpriv.h minimap.h bseq.h kalloc.h
 index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
 kalloc.o: kalloc.h
@@ -53,7 +54,7 @@ ksw2_extd2_sse.o: ksw2.h kalloc.h
 ksw2_exts2_sse.o: ksw2.h kalloc.h
 ksw2_extz2_sse.o: ksw2.h kalloc.h
 ksw2_ll_sse.o: ksw2.h kalloc.h
-main.o: bseq.h minimap.h mmpriv.h
+main.o: bseq.h minimap.h mmpriv.h getopt.h
 map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h
 misc.o: minimap.h ksort.h
 sdust.o: kalloc.h kdq.h kvec.h sdust.h
diff --git a/index.c b/index.c
index 80c302c..2123ab5 100644
--- a/index.c
+++ b/index.c
@@ -1,7 +1,7 @@
 #include <stdlib.h>
 #include <assert.h>
-#ifdef WIN32
-#include <io.h>
+#if defined(WIN32) || defined(_WIN32)
+#include <io.h> // for open(2)
 #else
 #include <unistd.h>
 #endif
diff --git a/kthread.c b/kthread.c
index 972aace..6004435 100644
--- a/kthread.c
+++ b/kthread.c
@@ -3,7 +3,7 @@
 #include <limits.h>
 #include <stdint.h>
 
-#ifdef WIN32
+#if defined(WIN32) || defined(_WIN32)
 #include <malloc.h>
 #define alloca _alloca
 #define __sync_fetch_and_add(ptr, addend)     _InterlockedExchangeAdd((void*)ptr, addend)
diff --git a/main.c b/main.c
index 0f2b014..01061a8 100644
--- a/main.c
+++ b/main.c
@@ -1,12 +1,6 @@
 #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"
@@ -14,15 +8,19 @@
 
 #define MM_VERSION "2.1-r316-dirty"
 
+#ifdef __linux__
+#include <sys/resource.h>
+#include <sys/time.h>
 void liftrlimit()
 {
-#ifdef __linux__
 	struct rlimit r;
 	getrlimit(RLIMIT_AS, &r);
 	r.rlim_cur = r.rlim_max;
 	setrlimit(RLIMIT_AS, &r);
-#endif
 }
+#else
+void liftrlimit() {}
+#endif
 
 static struct option long_options[] = {
 	{ "bucket-bits",    required_argument, 0, 0 },
diff --git a/misc.c b/misc.c
index c265ac1..d7dd1e4 100644
--- a/misc.c
+++ b/misc.c
@@ -96,7 +96,7 @@ double cputime()
 	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 */
+#endif /* WIN32 || _WIN32 */
 
 double realtime()
 {
diff --git a/sdust.c b/sdust.c
index 07339dd..f1e47e8 100644
--- a/sdust.c
+++ b/sdust.c
@@ -176,7 +176,7 @@ uint64_t *sdust(void *km, const uint8_t *seq, int l_seq, int T, int W, int *n)
 #ifdef _SDUST_MAIN
 #include <zlib.h>
 #include <stdio.h>
-#include <unistd.h>
+#include "getopt.h"
 #include "kseq.h"
 KSEQ_INIT(gzFile, gzread)
 
diff --git a/sketch.c b/sketch.c
index bdb5efb..ab3bcc8 100644
--- a/sketch.c
+++ b/sketch.c
@@ -5,7 +5,7 @@
 #include "kvec.h"
 #include "minimap.h"
 
-#ifdef WIN32
+#if defined(WIN32) || defined(_WIN32)
 #include <malloc.h>
 #define alloca _alloca
 #endif