--- slicetools-2.0.1.old/src/Coverage/alignSeqs.c	2005-08-04 16:32:29.000000000 +0200
+++ slicetools-2.0.1/src/Coverage/alignSeqs.c	2009-07-13 10:11:48.199857934 +0200
@@ -6,6 +6,7 @@
   construct a tiling of reads
 */
 
+
 #include "getCoverage.h"
 #define DEBUG 0
 
--- slicetools-2.0.1.old/src/Coverage/getCoverage.h	2005-08-04 16:32:29.000000000 +0200
+++ slicetools-2.0.1/src/Coverage/getCoverage.h	2009-07-13 09:55:08.486857187 +0200
@@ -15,11 +15,6 @@
 
 #include "config.h"
 
-#ifndef _LARGE_FILES
-#define ftello ftell
-#define fseeko fseek
-#endif
-
 #define MAXLINE     512 
 #define MAXSEQNAME  255
 #define MAXFILENAME 255
@@ -30,7 +25,6 @@
 #include <math.h>
 #include "Slice.h"
 
-#include <stdio.h>
 #include <stdlib.h>
 #include <ctype.h>
 #include <string.h>
--- slicetools-2.0.1.old/src/XMLTools/augmentSlice/TrimmedSequence.cc	2005-08-04 16:35:55.000000000 +0200
+++ slicetools-2.0.1/src/XMLTools/augmentSlice/TrimmedSequence.cc	2009-07-13 10:44:51.588119033 +0200
@@ -1,3 +1,5 @@
+#include <string.h>
+
 #include "TrimmedSequence.hh"
 
 TrimmedSequence::TrimmedSequence(const string & name)
--- slicetools-2.0.1.old/src/XMLTools/libXML/ContigAlign.hh	2005-08-04 16:40:05.000000000 +0200
+++ slicetools-2.0.1/src/XMLTools/libXML/ContigAlign.hh	2009-07-13 10:24:20.933856296 +0200
@@ -10,8 +10,8 @@
 class ContigAlign
 {
 public:
-  ContigAlign::ContigAlign(bool verbose);
-  virtual ContigAlign::~ContigAlign();
+  ContigAlign(bool verbose);
+  virtual ~ContigAlign();
 
 
   virtual int fattenLeft(Contig * contig,
--- slicetools-2.0.1.old/src/XMLTools/libXML/ContigFattener.hh	2005-08-04 16:40:05.000000000 +0200
+++ slicetools-2.0.1/src/XMLTools/libXML/ContigFattener.hh	2009-07-13 10:22:31.561858074 +0200
@@ -10,8 +10,8 @@
 class ContigFattener
 {
 public:
-  ContigFattener::ContigFattener(bool verbose);
-  ContigFattener::~ContigFattener();
+  ContigFattener(bool verbose);
+  ~ContigFattener();
 
   void addRead(Contig * contig, const string & seqname);
 
--- slicetools-2.0.1.old/src/XMLTools/libXML/SWAlign.cc	2005-08-04 16:40:05.000000000 +0200
+++ slicetools-2.0.1/src/XMLTools/libXML/SWAlign.cc	2009-07-13 10:44:03.732237091 +0200
@@ -1,3 +1,7 @@
+#include <iostream>
+#include <algorithm>
+#include <vector>
+
 #include "SWAlign.hh"
 
 // #define _DEBUG_VERBOSE 0
--- slicetools-2.0.1.old/src/XMLTools/libXML/SWAlign.hh	2005-08-04 16:40:05.000000000 +0200
+++ slicetools-2.0.1/src/XMLTools/libXML/SWAlign.hh	2009-07-13 10:25:15.180106208 +0200
@@ -6,8 +6,8 @@
 class SWAlign : public ContigAlign
 {
 public:
-  SWAlign::SWAlign(bool verbose);
-  SWAlign::~SWAlign();
+  SWAlign(bool verbose);
+  ~SWAlign();
 
   int fattenLeft(Contig * contig, ContigSequence * read, int distance);
   int fattenRight(Contig * contig, ContigSequence * read, int distance);
--- slicetools-2.0.1.old/src/libFoundation/ConfigFile.cc	2005-08-04 16:50:59.000000000 +0200
+++ slicetools-2.0.1/src/libFoundation/ConfigFile.cc	2009-07-13 10:54:00.553859579 +0200
@@ -28,6 +28,8 @@
  *  different values.
  */
 
+#include <string.h>
+
 #include "ConfigFile.hh"
 
 //! Constructor
--- slicetools-2.0.1.old/src/libFoundation/Exceptions.cc	2005-08-04 16:50:59.000000000 +0200
+++ slicetools-2.0.1/src/libFoundation/Exceptions.cc	2009-07-13 10:54:00.514858875 +0200
@@ -3,6 +3,8 @@
 //! @file 
 //! @brief Implements all exception classes
 
+#include <string.h>
+
 #include "Exceptions.hh"
 
 Exception::Exception(std::string msg, std::string module)
--- slicetools-2.0.1.old/src/libFoundation/Logger.cc	2005-08-04 16:50:59.000000000 +0200
+++ slicetools-2.0.1/src/libFoundation/Logger.cc	2009-07-13 10:54:00.598857273 +0200
@@ -52,6 +52,9 @@
  *  are independent of the filter level settings.
  */
 
+#include <stdio.h>
+#include <stdlib.h>
+
 #include "Logger.hh"
 
 //! Sets default values for class
--- slicetools-2.0.1.old/src/libFoundation/OptionResult.cc	2005-08-04 16:50:59.000000000 +0200
+++ slicetools-2.0.1/src/libFoundation/OptionResult.cc	2009-07-13 10:54:00.638858034 +0200
@@ -3,6 +3,9 @@
 //! @file 
 //! @brief OptionResult class implementation
 
+#include <stdio.h>
+#include <stdlib.h>
+
 #include "OptionResult.hh"
 
 //! Sets defaults for all results
--- slicetools-2.0.1.old/src/libFoundation/Options.cc	2005-08-04 16:50:59.000000000 +0200
+++ slicetools-2.0.1/src/libFoundation/Options.cc	2009-07-13 10:54:00.661858516 +0200
@@ -20,6 +20,8 @@
  *  written to stderr is prefixed with (stderr).
  */
 
+#include <string.h>
+
 #include "Options.hh"
 
 //! Constructor takes command line options in standard argc, argv format
--- slicetools-2.0.1.old/src/libFoundation/examples/example-configfile.cc	2005-08-04 16:51:00.000000000 +0200
+++ slicetools-2.0.1/src/libFoundation/examples/example-configfile.cc	2009-07-13 10:54:00.738857555 +0200
@@ -1,6 +1,9 @@
 // $Id: example-configfile.cc,v 1.1.1.1 2005/08/04 14:51:00 mcschatz Exp $
 // Demonstrates different techniques for handling configuration files
 
+#include <stdio.h>
+#include <stdlib.h>
+
 #include "Foundation.hh"
 using namespace std;
 
--- slicetools-2.0.1.old/src/libFoundation/examples/example-logging.cc	2005-08-04 16:51:00.000000000 +0200
+++ slicetools-2.0.1/src/libFoundation/examples/example-logging.cc	2009-07-13 10:54:00.723858021 +0200
@@ -1,6 +1,9 @@
 // $Id: example-logging.cc,v 1.1.1.1 2005/08/04 14:51:00 mcschatz Exp $
 // Demonstrates how Foundation logging can be used
 
+#include <stdio.h>
+#include <stdlib.h>
+
 #include "Foundation.hh"
 
 // Some functional section of the program.
--- slicetools-2.0.1.old/src/libFoundation/examples/example-minimal.cc	2005-08-04 16:51:00.000000000 +0200
+++ slicetools-2.0.1/src/libFoundation/examples/example-minimal.cc	2009-07-13 10:54:00.817857409 +0200
@@ -3,6 +3,9 @@
 
 
 // Only need to include the main header file
+#include <stdio.h>
+#include <stdlib.h>
+
 #include "Foundation.hh"
 using namespace std;
 
--- slicetools-2.0.1.old/src/libFoundation/examples/example-options.cc	2005-08-04 16:51:00.000000000 +0200
+++ slicetools-2.0.1/src/libFoundation/examples/example-options.cc	2009-07-13 10:54:00.778857616 +0200
@@ -1,6 +1,9 @@
 // $Id: example-options.cc,v 1.1.1.1 2005/08/04 14:51:00 mcschatz Exp $
 // Example program for options handling
 
+#include <stdio.h>
+#include <stdlib.h>
+
 #include "Foundation.hh"
 using namespace std;
 
--- slicetools-2.0.1.old/src/libSlice/ConsensusData.cc	2005-08-04 16:51:00.000000000 +0200
+++ slicetools-2.0.1/src/libSlice/ConsensusData.cc	2009-07-13 10:54:00.848871062 +0200
@@ -1,3 +1,5 @@
+#include <string.h>
+
 #include "ConsensusData.hh"
 
 namespace libSlice
--- slicetools-2.0.1.old/src/libSlice/SliceData.cc	2005-08-04 16:51:00.000000000 +0200
+++ slicetools-2.0.1/src/libSlice/SliceData.cc	2009-07-13 10:54:00.867108508 +0200
@@ -1,3 +1,5 @@
+#include <string.h>
+
 #include "SliceData.hh"
 #include <stdlib.h>  // for atol