tigr-glimmer (3.02-2) 10_gcc4.3.patch

Summary

 src/Common/delcher.cc           |    1 +
 src/Common/fasta.cc             |    2 +-
 src/Common/gene.cc              |    1 +
 src/Glimmer/anomaly.cc          |    1 +
 src/Glimmer/glimmer2.cc         |    1 +
 src/Glimmer/glimmer3.cc         |    3 +--
 src/Glimmer/long-orfs.cc        |    2 +-
 src/ICM/build-fixed.cc          |    1 +
 src/ICM/build-icm.cc            |    1 +
 src/ICM/icm.cc                  |    2 ++
 src/ICM/score-fixed.cc          |    1 +
 src/Util/entropy-score.cc       |    2 +-
 src/Util/extract.cc             |    2 +-
 src/Util/multi-extract.cc       |    2 +-
 src/Util/start-codon-distrib.cc |    1 +
 src/Util/uncovered.cc           |    2 +-
 16 files changed, 17 insertions(+), 8 deletions(-)

    
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Patch contents

Author: Kumar Appaiah
Description: Fix #461691

--- 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"