From 543fa12e6890c2aee28e09f638e80397f90350bc Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 19 Jan 2018 10:40:18 -0500
Subject: [PATCH] r659: for C++ compatibility

---
 bseq.c    | 1 +
 index.c   | 1 +
 kthread.c | 1 +
 main.c    | 2 +-
 misc.c    | 2 +-
 sketch.c  | 3 ++-
 6 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/bseq.c b/bseq.c
index 9b4800f..dc6b75f 100644
--- a/bseq.c
+++ b/bseq.c
@@ -2,6 +2,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <assert.h>
+#define __STDC_LIMIT_MACROS
 #include "bseq.h"
 #include "kvec.h"
 #include "kseq.h"
diff --git a/index.c b/index.c
index e388ad7..60cdf5b 100644
--- a/index.c
+++ b/index.c
@@ -7,6 +7,7 @@
 #endif
 #include <fcntl.h>
 #include <stdio.h>
+#define __STDC_LIMIT_MACROS
 #include "kthread.h"
 #include "bseq.h"
 #include "minimap.h"
diff --git a/kthread.c b/kthread.c
index 249ceea..ffdf940 100644
--- a/kthread.c
+++ b/kthread.c
@@ -2,6 +2,7 @@
 #include <stdlib.h>
 #include <limits.h>
 #include <stdint.h>
+#include "kthread.h"
 
 #if (defined(WIN32) || defined(_WIN32)) && defined(_MSC_VER)
 #define __sync_fetch_and_add(ptr, addend)     _InterlockedExchangeAdd((void*)ptr, addend)
diff --git a/main.c b/main.c
index 0768aa3..8779282 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.7-r658-dirty"
+#define MM_VERSION "2.7-r659-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/misc.c b/misc.c
index a846d1e..2667e2b 100644
--- a/misc.c
+++ b/misc.c
@@ -1,4 +1,4 @@
-#include "minimap.h"
+#include "mmpriv.h"
 
 int mm_verbose = 1;
 int mm_dbg_flag = 0;
diff --git a/sketch.c b/sketch.c
index 7fc5352..f830693 100644
--- a/sketch.c
+++ b/sketch.c
@@ -2,8 +2,9 @@
 #include <stdlib.h>
 #include <assert.h>
 #include <string.h>
+#define __STDC_LIMIT_MACROS
 #include "kvec.h"
-#include "minimap.h"
+#include "mmpriv.h"
 
 unsigned char seq_nt4_table[256] = {
 	0, 1, 2, 3,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,