Index: head/biology/lagan/files/patch-src__glocal__rightinfluence.cpp
===================================================================
--- head/biology/lagan/files/patch-src__glocal__rightinfluence.cpp	(revision 415035)
+++ head/biology/lagan/files/patch-src__glocal__rightinfluence.cpp	(revision 415036)
@@ -1,32 +1,33 @@
---- src/glocal/rightinfluence.cpp.orig
+--- src/glocal/rightinfluence.cpp.orig	2006-09-14 20:40:19 UTC
 +++ src/glocal/rightinfluence.cpp
 @@ -1,6 +1,6 @@
  #include <rightinfluence.h>
  
 -Fragment origin, end;
 +Fragment origin, my_end;
  
  // Sets the first default owner of the whole region
  void initRI(RI *RightInfluence, long long int scoreIndex) {
-@@ -18,17 +18,17 @@
+@@ -18,17 +18,17 @@ void initRI(RI *RightInfluence, long lon
  
  	// hack to aid winner selection
  	origin.score = -1;
 -	end.score = -2;
 -	origin.totalScore = end.totalScore = 0;
 +	my_end.score = -2;
 +	origin.totalScore = my_end.totalScore = 0;
  
  	// will win against anyone
 -	end.seq1End = 0; end.seq2End = 0;
 -	end.seq1Start = 0; end.seq2Start = 0;
 +	my_end.seq1End = 0; my_end.seq2End = 0;
 +	my_end.seq1Start = 0; my_end.seq2Start = 0;
  
  	origin.back = NULL;
  
      RightInfluence->act[-INF] = &origin;
 -    RightInfluence->act[+INF] = &end;
 +    RightInfluence->act[+INF] = &my_end;
  }
+ 
  
Index: head/biology/lagan/files/patch-src__glocal__score.cpp
===================================================================
--- head/biology/lagan/files/patch-src__glocal__score.cpp	(revision 415035)
+++ head/biology/lagan/files/patch-src__glocal__score.cpp	(revision 415036)
@@ -1,11 +1,11 @@
---- src/glocal/score.cpp.orig	2006-09-15 05:40:19.000000000 +0900
-+++ src/glocal/score.cpp	2012-10-03 00:22:50.000000000 +0900
+--- src/glocal/score.cpp.orig	2006-09-14 20:40:19 UTC
++++ src/glocal/score.cpp
 @@ -2,7 +2,7 @@
  #include<score.h>
  #include<leftinfluence.h>
  #include<rightinfluence.h>
 -#include<fstream.h>
 +#include<fstream>
  
  extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
  
Index: head/biology/lagan/files/patch-src__utils__Glue.cpp
===================================================================
--- head/biology/lagan/files/patch-src__utils__Glue.cpp	(revision 415035)
+++ head/biology/lagan/files/patch-src__utils__Glue.cpp	(revision 415036)
@@ -1,10 +1,10 @@
---- src/utils/Glue.cpp.orig	2006-09-15 05:40:18.000000000 +0900
-+++ src/utils/Glue.cpp	2012-10-03 00:23:38.000000000 +0900
+--- src/utils/Glue.cpp.orig	2006-09-14 20:40:18 UTC
++++ src/utils/Glue.cpp
 @@ -6,6 +6,7 @@
  #include <fstream>
  #include <iostream>
  #include <algorithm>
 +#include <cstring>
  
  #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
  #define MAX_LINE_LENGTH 1024
Index: head/biology/lagan/files/patch-src_anchors.c
===================================================================
--- head/biology/lagan/files/patch-src_anchors.c	(nonexistent)
+++ head/biology/lagan/files/patch-src_anchors.c	(revision 415036)
@@ -0,0 +1,20 @@
+--- src/anchors.c.orig	2016-05-11 21:46:55 UTC
++++ src/anchors.c
+@@ -225,7 +225,7 @@ char* rolltonum(char* str) {
+   return &str[i];
+ }
+ 
+-int getline(FILE* infile, hll* tt) {
++int get_line(FILE* infile, hll* tt) {
+   char temp[1024];
+   char* help;
+   int z, h;
+@@ -248,7 +248,7 @@ hll* parseCHAOS(FILE* infile, int* totnu
+   *totnum = 0;
+   while(!feof(infile)) {
+     tt = (hll*) malloc(sizeof(hll));
+-    while (!feof(infile) && !getline(infile, tt))
++    while (!feof(infile) && !get_line(infile, tt))
+       ;
+     if (feof(infile)) break;
+     if (gapfreechunks) {

Property changes on: head/biology/lagan/files/patch-src_anchors.c
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Added: fbsd:nokeywords
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+yes
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