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diff -urN fragrep-2/aln2pattern.cpp fragrep-2a/aln2pattern.cpp
--- fragrep-2/aln2pattern.cpp 2007-06-04 08:09:49.000000000 +0200
+++ fragrep-2a/aln2pattern.cpp 2015-09-19 14:55:19.742905181 +0200
@@ -8,6 +8,8 @@
#include <vector>
#include <fstream>
#include <iomanip>
+#include <cstring>
+#include <stdlib.h>
#include "math.h"
#include "eps_output.h"
diff -urN fragrep-2/eps_output.cpp fragrep-2a/eps_output.cpp
--- fragrep-2/eps_output.cpp 2007-06-04 08:09:49.000000000 +0200
+++ fragrep-2a/eps_output.cpp 2015-09-19 14:55:55.526022481 +0200
@@ -4,6 +4,7 @@
#include <cstdio>
#include <fstream>
#include <iomanip>
+#include <algorithm>
#include "math.h"
namespace fragrep
diff -urN fragrep-2/fragrep.cpp fragrep-2a/fragrep.cpp
--- fragrep-2/fragrep.cpp 2007-06-04 08:09:49.000000000 +0200
+++ fragrep-2a/fragrep.cpp 2015-09-19 14:51:12.064400495 +0200
@@ -2,6 +2,8 @@
fragrep c++ rebuild */
// std and iostream headers
+#include <stdlib.h>
+#include <cstring>
#include <ctype.h>
#include <iostream>
#include <fstream>
diff -urN fragrep-2/omit_pattern_matching.cpp fragrep-2a/omit_pattern_matching.cpp
--- fragrep-2/omit_pattern_matching.cpp 2007-06-04 08:09:49.000000000 +0200
+++ fragrep-2a/omit_pattern_matching.cpp 2015-09-19 14:51:34.200933515 +0200
@@ -12,6 +12,7 @@
#include <list>
#include <vector>
+#include <cstring>
#include <string>
#include <algorithm>
#include <sequtil/triple.h>
Binary files fragrep-2/pattern2eps and fragrep-2a/pattern2eps differ
diff -urN fragrep-2/pattern2eps.cpp fragrep-2a/pattern2eps.cpp
--- fragrep-2/pattern2eps.cpp 2007-06-04 08:09:49.000000000 +0200
+++ fragrep-2a/pattern2eps.cpp 2015-09-19 14:56:23.245855128 +0200
@@ -7,7 +7,9 @@
#include <fstream>
#include <list>
#include <stdio.h>
+#include <stdlib.h>
#include <map>
+#include <cstring>
#include <string>
#include <sstream>
diff -urN fragrep-2/pattern_matching.cpp fragrep-2a/pattern_matching.cpp
--- fragrep-2/pattern_matching.cpp 2007-06-04 08:09:49.000000000 +0200
+++ fragrep-2a/pattern_matching.cpp 2015-09-19 14:55:37.502797959 +0200
@@ -12,6 +12,7 @@
#include <list>
#include <vector>
+#include <cstring>
#include <string>
#include <algorithm>
#include <sequtil/triple.h>
diff -urN fragrep-2/sequtil/fasta.cpp fragrep-2a/sequtil/fasta.cpp
--- fragrep-2/sequtil/fasta.cpp 2007-06-04 08:09:49.000000000 +0200
+++ fragrep-2a/sequtil/fasta.cpp 2015-09-19 14:53:01.977070250 +0200
@@ -3,6 +3,7 @@
#include <iostream>
+#include <algorithm>
#include "fasta.h"
#include "bbq_util.h"
diff -urN fragrep-2/sequtil/position_weight_matrix.cpp fragrep-2a/sequtil/position_weight_matrix.cpp
--- fragrep-2/sequtil/position_weight_matrix.cpp 2007-06-04 08:09:49.000000000 +0200
+++ fragrep-2a/sequtil/position_weight_matrix.cpp 2015-09-19 14:54:44.999781603 +0200
@@ -3,6 +3,10 @@
#include "bbq_util.h"
#include <list>
#include <math.h>
+#include <stdlib.h>
+#include <cstring>
+#include <climits>
+#include <algorithm>
#include <limits>
#include <float.h>
#include <iomanip>
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