From a4647ea20eb055dea32af7927b23329994d60163 Mon Sep 17 00:00:00 2001
From: Olivier Cinquin <olivier@brutus1.bio.uci.edu>
Date: Sun, 7 Sep 2014 18:26:27 -0700
Subject: [PATCH] Allow compilation with FreeBSD/clang.
---
src/fisher/kfunc.c | 4 ++--
src/utils/BamTools/src/api/internal/io/HostInfo_p.cpp | 3 +++
.../BamTools/src/api/internal/io/TcpSocketEngine_unix_p.cpp | 4 +++-
3 files changed, 8 insertions(+), 3 deletions(-)
diff --git a/src/fisher/kfunc.c b/src/fisher/kfunc.c
index e735e636..5c39d497 100644
--- a/src/fisher/kfunc.c
+++ b/src/fisher/kfunc.c
@@ -1,4 +1,4 @@
-#include <math.h>
+#include <cmath>
#include <stdlib.h>
/* Log gamma function
@@ -243,7 +243,7 @@ double kt_fisher_exact(long long n11, long long n12, long long n21, long long n2
*two = left + right;
if (*two > 1.) *two = 1.;
// adjust left and right
- if (abs(i - n11) < abs(j - n11)) right = 1. - left + q;
+ if (abs((long) (i - n11)) < abs((long) (j - n11))) right = 1. - left + q;
else left = 1.0 - right + q;
*_left = left; *_right = right;
return q;
diff --git a/src/utils/BamTools/src/api/internal/io/HostInfo_p.cpp b/src/utils/BamTools/src/api/internal/io/HostInfo_p.cpp
index 40b10472..5248e63d 100644
--- a/src/utils/BamTools/src/api/internal/io/HostInfo_p.cpp
+++ b/src/utils/BamTools/src/api/internal/io/HostInfo_p.cpp
@@ -7,6 +7,9 @@
// Provides DNS lookup functionality for hostname & its discovered addresses
// ***************************************************************************
+#ifdef __FreeBSD__
+#include <netinet/in.h>
+#endif
#include "api/internal/io/HostInfo_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
diff --git a/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_unix_p.cpp b/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_unix_p.cpp
index 5b100e48..58994077 100644
--- a/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_unix_p.cpp
+++ b/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_unix_p.cpp
@@ -6,7 +6,9 @@
// ---------------------------------------------------------------------------
// Provides low-level implementation of TCP I/O for all UNIX-like systems
// ***************************************************************************
-
+#ifdef __FreeBSD__
+#include <netinet/in.h>
+#endif
#include "api/internal/io/TcpSocketEngine_p.h"
#include "api/internal/io/NetUnix_p.h"
using namespace BamTools;
--
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