v10.8 - minimalCoveragePerPosition bug corrected

Author: valeu

scripts/assess_significance.R

@@ -1,3 +1,5 @@
+#!/usr/bin/env Rscript
+
 library(rtracklayer)
 
 args <- commandArgs()

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;

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;

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;

scripts/makeGraph.R

@@ -1,3 +1,5 @@
+#!/usr/bin/env Rscript
+
 args <- commandArgs()
 
 dataTable <-read.table(args[5], header=TRUE);

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])

src/freec

@@ -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";
 	}

src/main.cpp

@@ -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