Merge branch 'release/3.0.0'

* Use version 2.2.5 of the battenberg R package
* Removed R files from repository

.travis.yml

@@ -45,3 +45,6 @@ script:
  - ./setup.sh $HOME/alleleCount-opt $HOME/cgpVcf-opt/lib/perl5:$HOME/PCAP-opt/lib/perl5
  - cd ../
  - ./setup.sh $HOME/cgpBattenberg-opt $HOME/alleleCount-opt/lib/perl5:$HOME/cgpVcf-opt/lib/perl5:$HOME/PCAP-opt/lib/perl5
+
+dist: trusty
+sudo: false

CHANGES.md

@@ -0,0 +1,3 @@
+### 3.0.0
+* Use verion 2.2.5 of the battenberg R package
+* Removed R files from repository

README.md

@@ -3,11 +3,13 @@ cgpBattenberg
 
 An installation helper, perl wrapper and the R program Battenberg which detects subclonality and copy number in matched NGS data.
 
-[![Build Status](https://travis-ci.org/cancerit/cgpBattenberg.svg?branch=master)](https://travis-ci.org/cancerit/cgpBattenberg) : master  
+[![Build Status](https://travis-ci.org/cancerit/cgpBattenberg.svg?branch=master)](https://travis-ci.org/cancerit/cgpBattenberg) : master
 [![Build Status](https://travis-ci.org/cancerit/cgpBattenberg.svg?branch=dev)](https://travis-ci.org/cancerit/cgpBattenberg) : dev
 
 ## Installation
 
+The battenberg R files are not included in this repository. The perl wrapper supports battenberg v2.2.5 and this will be made publically available by the authors shortly. The last version of this repository to include the battenberg R files is 1.5.3
+
 Please install the following before attempting to run ``setup.sh <install_to_folder> [X/lib/perl:Y/lib/perl]``
 
 1. [PCAP-core v2.1.3+](https://github.com/ICGC-TCGA-PanCancer/PCAP-core/releases)

perl/bin/battenberg.pl

@@ -63,6 +63,7 @@
 const my $DEFAULT_PROTOCOL => 'WGS';
 const my $DEFAULT_PLATFORM => 'ILLUMINA';
 const my $DEFAULT_SEED => 1488823153;
+const my $DEFAULT_CALC_SEG_BAF_OPTION => 2; #Options are: 1 - median, 2 - mean.
 
 const my $SPLIT_LOCI_ALL_GLOB => q{1000genomesloci2012_chr*_split*.txt};
 
@@ -190,6 +191,7 @@ sub setup {
           'nc|noclean' => \$opts{'noclean'},
           'nl|num_loci_files=i' => \$opts{'num_loci_files'},
           'se|seed=i' => \$opts{'seed'},
+          'sb|calc_seg_baf_option=i' => \$opts{'calc_seg_baf_option'},
 		) or pod2usage(2);
 
 	pod2usage(-verbose => 0, -exitval => 0) if(defined $opts{'h'});
@@ -394,7 +396,11 @@ sub setup {
 	$opts{'platform'} = $DEFAULT_PLATFORM if(!exists($opts{'platform'}) || !defined($opts{'platform'}));
 
   $opts{'seed'} = $DEFAULT_SEED if(!exists($opts{'seed'}) || !defined($opts{'seed'}));
+  $opts{'calc_seg_baf_option'} = $DEFAULT_CALC_SEG_BAF_OPTION if(!exists($opts{'calc_seg_baf_option'}) || !defined($opts{'calc_seg_baf_option'}));
 
+  if ($opts{'calc_seg_baf_option'} < 1 || $opts{'calc_seg_baf_option'} > 2) {
+    die "ERROR: calc_seg_baf_option (" . $opts{'calc_seg_baf_option'} . ") can have values 1 (median) or 2 (mean)\n";
+  }
 	return \%opts;
 }
 
@@ -450,6 +456,7 @@ =head1 SYNOPSIS
     -genderloci            -gl  List of gender loci, required when '-ge L' [share/gender/GRCh37d5_Y.loci]
                                 - these are loci that will not present at all in a female sample
     -seed                  -se Integer value to be used as a seed for random number generation [1488823153]
+    -calc_seg_baf_option   -sb Various options to recalculate the BAF of a segment. Options are: 1 - median, 2 - mean. (Default: 2)
 
    Optional system related parameters:
     -threads           -t   Number of threads allowed on this machine (default 1)

perl/lib/Sanger/CGP/Battenberg/Implement.pm

@@ -166,7 +166,6 @@ const my $SEGMENTATION_GAMMA => 10;
 const my $PHASING_GAMMA => 1;
 const my $KMIN => 3;
 const my $PHASE_KMIN => 3;
-const my $CALC_SEG_BAF_OPTION => 1;
 
 #callsubclones
 const my $SIGLEVEL => 0.05;
@@ -800,7 +799,7 @@ sub battenberg_segmentphased{
   my $phasegamma = $PHASING_GAMMA;
   my $kmin = $KMIN;
   my $phasekmin = $PHASE_KMIN;
-  my $calc_seg_baf_option = $CALC_SEG_BAF_OPTION;
+  my $calc_seg_baf_option = $options->{'calc_seg_baf_option'};
 
 	my $command = "cd $tmp; ";
 	$command .= _which($RSCRIPT) || die "Unable to find $RSCRIPT in path";
@@ -855,13 +854,11 @@ sub battenberg_fitcopyno{
   }
   my $rho_psi_cmds = q{};
   if (exists ($options->{'rho'}) && defined($options->{'rho'})){
-    #Sanity checks for psi and rho
-    #if ($options->{'rho'} < $options->{'min_rho'} || $options->{'rho'} > $options->{'max_rho'}) {
-    #  die("Invalid value for rho (" . $options->{'rho'} . "). This should be in the range specified by min_rho (" . $options->{'min_rho'} . ") and max_rho (" . $options->{'max_rho'} . ")");
-    #}
-    #if ($options->{'psi'} < $options->{'min_ploidy'} || $options->{'psi'} > $options->{'max_ploidy'}) {
-    #  die("Invalid value for ploidy (" . $options->{'psi'} . "). This should be in the range specified by min_ploidy (" . $options->{'min_ploidy'} . ") and max_ploidy (" . $options->{'max_ploidy'} . ")");
-    #}
+    #Sanity checks for rho only. Truncate to 5 decimal places for max comparison to allow for rounding issues
+    my $round_rho = sprintf("%.5f", $options->{'rho'});
+    if ($options->{'rho'} < $options->{'min_rho'} || $round_rho > $options->{'max_rho'}) {
+      die("Invalid value for rho (" . $round_rho . "). This should be in the range specified by min_rho (" . $options->{'min_rho'} . ") and max_rho (" . $options->{'max_rho'} . ")");
+    }
     $rho_psi_cmds .= ', use_preset_rho_psi=T';
     $rho_psi_cmds .= ', preset_rho='. $options->{'rho'};
     $rho_psi_cmds .= ', preset_psi=' . $options->{'psi'};
@@ -966,7 +963,7 @@ sub battenberg_callsubclones{
   my $siglevel = $SIGLEVEL;
   my $maxdist = $MAXDIST;
   my $noperms = $NOPERMS;
-  my $calc_seg_baf_option = $CALC_SEG_BAF_OPTION;
+  my $calc_seg_baf_option = $options->{'calc_seg_baf_option'};
   my $seed = $options->{'seed'};
 
 	my $command = "cd $tmp; ";