diff --git a/scripts/assess_significance.R b/scripts/assess_significance.R
index f466024..4193d97 100644
--- a/scripts/assess_significance.R
+++ b/scripts/assess_significance.R
@@ -1,3 +1,5 @@
+#!/usr/bin/env Rscript
+
 library(rtracklayer)
 
 args <- commandArgs()
diff --git a/scripts/freec2bed.pl b/scripts/freec2bed.pl
index 431929f..6b74c03 100644
--- a/scripts/freec2bed.pl
+++ b/scripts/freec2bed.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl -w
 #translate *_ratio.txt (the out put of FREEC) into a BED track
 
 use strict;
diff --git a/scripts/freec2circos.pl b/scripts/freec2circos.pl
index 6945256..d1569e7 100644
--- a/scripts/freec2circos.pl
+++ b/scripts/freec2circos.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl -w
 #translate "*_ratio.txt" (output of FREEC) into a Circos track
 
 use strict;
diff --git a/scripts/get_fasta_lengths.pl b/scripts/get_fasta_lengths.pl
index 97c889a..b45ce78 100644
--- a/scripts/get_fasta_lengths.pl
+++ b/scripts/get_fasta_lengths.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl -w
 #prints lengths of sequences from a multifasta file
 
 use strict;
diff --git a/scripts/makeGraph.R b/scripts/makeGraph.R
index 6510fff..9938587 100644
--- a/scripts/makeGraph.R
+++ b/scripts/makeGraph.R
@@ -1,3 +1,5 @@
+#!/usr/bin/env Rscript
+
 args <- commandArgs()
 
 dataTable <-read.table(args[5], header=TRUE);
diff --git a/scripts/makeGraph_Chromosome.R b/scripts/makeGraph_Chromosome.R
index 2091fd0..8bd2dcb 100644
--- a/scripts/makeGraph_Chromosome.R
+++ b/scripts/makeGraph_Chromosome.R
@@ -1,3 +1,4 @@
+<<<<<<< HEAD
 path = "/data/tmp/cgurjao/Graphical_outputs/R\ scripts/FREEC_7.4/Single-end"
 setwd(path)
 
@@ -10,6 +11,14 @@ args[4] = 1
 
 dataTable <-read.table(args[6], header=T, na.strings="NA");
 print(paste (args[6],"read"))
+=======
+#!/usr/bin/env Rscript
+
+args <- commandArgs()
+
+dataTable <-read.table(args[6], header=TRUE);
+print( paste (args[6],"read"))
+>>>>>>> 76030ffbfebd715b07a1c240056a37cb02bbb1ff
 ratio<-data.frame(dataTable)
 chr <- type.convert(args[4])
 ploidy <- type.convert(args[5])
diff --git a/src/freec b/src/freec
index b234400..d034afd 100644
Binary files a/src/freec and b/src/freec differ
diff --git a/src/main.cpp b/src/main.cpp
index 4822eb1..381adbe 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -255,7 +255,7 @@ int main(int argc, char *argv[])
             }
     }
 
-	int minimalTotalLetterCountPerPosition = round_f(float(cf.Value("general","minimalCoveragePerPosition", 0)));
+	int minimalTotalLetterCountPerPosition = round_f(float(cf.Value("BAF","minimalCoveragePerPosition", 0)));
 	if (minimalTotalLetterCountPerPosition>0) {
         cout << "..will use a threshold of "<< minimalTotalLetterCountPerPosition <<" read(s) per SNP position to calculate beta allel frequency (BAF) values\n";
 	}
diff --git a/src/version.h b/src/version.h
index 1982453..7c1053a 100644
--- a/src/version.h
+++ b/src/version.h
@@ -3,7 +3,7 @@
 #define VERSION_H
 
 const double VERSION_OFFSET = 3;
-const double FREEC_VERSION = 10.7;
+const double FREEC_VERSION = 10.8;
 const double CONTROL_FREEC_VERSION = FREEC_VERSION - VERSION_OFFSET;
 
 #endif