From e5a491c13ff43d7e21eaa692e86a94ecdf0b0ac7 Mon Sep 17 00:00:00 2001
From: Aaron Quinlan <aaronquinlan@gmail.com>
Date: Fri, 24 Apr 2009 15:02:21 -0400
Subject: [PATCH] Updated includes to ease compilation on other systems.

	1.  Thanks to Loyal Goff at CSAIL/Broad for help identifying misssing includes.
	2.  Updated README to reflect this.
---
 README                                      | 5 ++++-
 src/complementBed/Makefile                  | 3 ++-
 src/complementBed/complementBed.h           | 3 ++-
 src/coverageBed/coverageBed.h               | 7 ++++---
 src/utils/bedFile/bedFile.h                 | 1 +
 src/utils/sequenceUtilities/sequenceUtils.h | 2 ++
 6 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/README b/README
index 62855b3e..129a7ebd 100644
--- a/README
+++ b/README
@@ -35,10 +35,13 @@ available on the Galaxy website.  I merely found it too slow to do several itera
 especially with large sequencing datasets.  Regardless, I am grateful to the Galaxy team for creating such a
 useful site that is rapidly approaching ubiquity.
 
-4.  Ira Hall.
+4.  Ira Hall, UVa.
 Discussion between Ira and I are largely the motivation for these tools.  We are frequently tracking 
 down impromptu ideas and these tools were largely designed to facilitate tangents.
 
+5. Loyal Goff, CSAIL, Broad.
+Many thanks to Loyal for his assistance in making BED Tools "compilable" on the SUSE platform.  I appreciate your help and patience.
+
 
 ===Requests===
 I would be grateful to learn of any problems or suggestions you have for improving these tools.
diff --git a/src/complementBed/Makefile b/src/complementBed/Makefile
index 8f9b7952..d3a6b749 100755
--- a/src/complementBed/Makefile
+++ b/src/complementBed/Makefile
@@ -1,6 +1,7 @@
 CXX = g++
 CXXFLAGS = -O3
 LDFLAGS = 
+LIBFLAGS = -lc
 
 UTILITIES_DIR = ../utils/
 OBJ_DIR = ../../obj/
@@ -28,7 +29,7 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
+	@$(CXX) $(LIBFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
diff --git a/src/complementBed/complementBed.h b/src/complementBed/complementBed.h
index bcdbb0b2..1e9cb788 100755
--- a/src/complementBed/complementBed.h
+++ b/src/complementBed/complementBed.h
@@ -5,7 +5,8 @@
 #include <list>
 #include <iostream>
 #include <fstream>
-#include <limits>
+#include <limits.h>
+#include <stdlib.h>
 
 using namespace std;
 
diff --git a/src/coverageBed/coverageBed.h b/src/coverageBed/coverageBed.h
index f3ab16d3..8504c337 100755
--- a/src/coverageBed/coverageBed.h
+++ b/src/coverageBed/coverageBed.h
@@ -1,5 +1,5 @@
-#ifndef GRAPHBED_H
-#define GRAPHBED_H
+#ifndef	COVERAGEBED_H
+#define COVERAGEBED_H
 
 #include "bedFile.h"
 #include <vector>
@@ -7,6 +7,7 @@
 #include <list>
 #include <iostream>
 #include <fstream>
+#include <stdlib.h>
 
 using namespace std;
 
@@ -42,4 +43,4 @@ private:
 	BedFile *bedA, *bedB;
 
 };
-#endif /* GRAPHBED_H */
+#endif /* COVERAGEBED_H */
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index 3cabeb4c..bfc192f5 100755
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -8,6 +8,7 @@
 #include <fstream>
 #include <sstream>
 #include <cstring>
+#include <algorithm>
 
 using namespace std;
 
diff --git a/src/utils/sequenceUtilities/sequenceUtils.h b/src/utils/sequenceUtilities/sequenceUtils.h
index 1254e7e4..1635d49d 100644
--- a/src/utils/sequenceUtilities/sequenceUtils.h
+++ b/src/utils/sequenceUtilities/sequenceUtils.h
@@ -2,6 +2,8 @@
 #define SEQUENCEUTILS_H
 
 #include <string>
+#include <algorithm>
+
 using namespace std;
 
 // Performs an in-place sequence reversal
-- 
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