--- glimmer3.02.orig/src/Common/delcher.cc
+++ glimmer3.02/src/Common/delcher.cc
@@ -9,6 +9,7 @@
#include "delcher.hh"
+#include <cstring>
const int COMMATIZE_BUFF_LEN = 50;
// Length of buffer for creating string with commas
--- glimmer3.02.orig/src/Common/fasta.cc
+++ glimmer3.02/src/Common/fasta.cc
@@ -9,7 +9,7 @@
#include "fasta.hh"
-
+#include <cstring>
void Fasta_Print
(FILE * fp, const char * s, const char * hdr, int fasta_width)
--- glimmer3.02.orig/src/Common/gene.cc
+++ glimmer3.02/src/Common/gene.cc
@@ -10,6 +10,7 @@
#include "delcher.hh"
#include "gene.hh"
+#include <cstring>
static const char COMPLEMENT_TABLE []
= "nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"
--- glimmer3.02.orig/src/Glimmer/anomaly.cc
+++ glimmer3.02/src/Glimmer/anomaly.cc
@@ -12,6 +12,7 @@
#include "anomaly.hh"
+#include <cstring>
// Global variables
--- glimmer3.02.orig/src/ICM/icm.cc
+++ glimmer3.02/src/ICM/icm.cc
@@ -15,6 +15,8 @@
#include "icm.hh"
+#include <cstring>
+
using namespace std;
extern int Verbose;
--- glimmer3.02.orig/src/Util/entropy-score.cc
+++ glimmer3.02/src/Util/entropy-score.cc
@@ -9,7 +9,7 @@
// regions in it by entropy distance. Results are output
// to stdout .
-
+#include <cstring>
#include "entropy-score.hh"
--- glimmer3.02.orig/src/Glimmer/glimmer3.cc
+++ glimmer3.02/src/Glimmer/glimmer3.cc
@@ -12,11 +12,10 @@
// Copyright (c) 2006 University of Maryland Center for Bioinformatics
// & Computational Biology
-
+#include <cstring>
#include "glimmer3.hh"
-
static int For_Edwin = 0;
--- glimmer3.02.orig/src/ICM/build-icm.cc
+++ glimmer3.02/src/ICM/build-icm.cc
@@ -13,6 +13,7 @@
#include "build-icm.hh"
+#include <cstring>
static int Genbank_Xlate_Code = 0;
// Holds the Genbank translation table number that determines
--- glimmer3.02.orig/src/Util/extract.cc
+++ glimmer3.02/src/Util/extract.cc
@@ -9,7 +9,7 @@
// sequences specified by coordinates. The resulting sequences
// are output (in multifasta or two-string format) to stdout.
-
+#include <cstring>
#include "extract.hh"
--- glimmer3.02.orig/src/Glimmer/glimmer2.cc
+++ glimmer3.02/src/Glimmer/glimmer2.cc
@@ -37,6 +37,7 @@
#include "delcher.h"
#include "gene.h"
+#include <cstring>
const int DEFAULT_MIN_GENE_LEN = 90;
const double DEFAULT_MIN_OLAP_PERCENT = 0.10;
--- glimmer3.02.orig/src/Glimmer/long-orfs.cc
+++ glimmer3.02/src/Glimmer/long-orfs.cc
@@ -15,7 +15,7 @@
#include "long-orfs.hh"
-
+#include <cstring>
// External variables
--- glimmer3.02.orig/src/ICM/build-fixed.cc
+++ glimmer3.02/src/ICM/build-fixed.cc
@@ -12,6 +12,7 @@
#include "build-fixed.hh"
+#include <cstring>
static FILE * Index_File_fp = NULL;
// File containing a list of subscripts of strings to train model
--- glimmer3.02.orig/src/ICM/score-fixed.cc
+++ glimmer3.02/src/ICM/score-fixed.cc
@@ -8,6 +8,7 @@
#include "score-fixed.hh"
+#include <cstring>
static char * Pos_Model_Path;
// Name of file containing the positive model
--- glimmer3.02.orig/src/Util/multi-extract.cc
+++ glimmer3.02/src/Util/multi-extract.cc
@@ -10,7 +10,7 @@
// resulting sequences are output (in multifasta or two-string format)
// to stdout.
-
+#include <cstring>
#include "multi-extract.hh"
--- glimmer3.02.orig/src/Util/start-codon-distrib.cc
+++ glimmer3.02/src/Util/start-codon-distrib.cc
@@ -17,6 +17,7 @@
#include "start-codon-distrib.hh"
+#include <cstring>
// External variables
--- glimmer3.02.orig/src/Util/uncovered.cc
+++ glimmer3.02/src/Util/uncovered.cc
@@ -10,7 +10,7 @@
// specified in the file named as the second command-line argument.
// Output is a multifasta file sent to stdout.
-
+#include <cstring>
#include "uncovered.hh"