Merge branch 'hotfix/3.5.3'

cancerit · Jan 10, 2020 · 628a58c · 628a58c
2 parents 5355d2a + 9372593
commit 628a58c
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,15 @@
 # Changes
 
+## 3.5.3
+
+* Fix parsing of subclones file when generating final outputs
+* This release points to cancerit fork of core battenberg algorithm [here](https://github.com/cancerit/battenberg/feature/grch38)
+  * v2.3.1 - faster PCF function
+
+## 3.5.2
+
+* Fix parsing of subclones file during refit
+
 ## 3.5.1
 
 * Fix #107, again... solves the problem of Rprofile not being found when container invoked by tools that mess with $HOME

diff --git a/Rsupport/setupR.sh b/Rsupport/setupR.sh
@@ -41,7 +41,7 @@ INST_PATH=$1
 BUILD_R=$2
 
 VERSION_ASCAT='2.5.1' # no 'v', not a project archive an artifact
-VERSION_BB='v2.3.0' # with 'v', this is a project archive
+VERSION_BB='v2.3.1' # with 'v', this is a project archive
 
 CPU=`grep -c ^processor /proc/cpuinfo`
 if [ $? -eq 0 ]; then

diff --git a/perl/bin/battenberg_CN_to_VCF.pl b/perl/bin/battenberg_CN_to_VCF.pl
@@ -110,7 +110,7 @@ BEGIN
     while(<$IN_FH>){
       my $line = $_;
       chomp($line);
-      next if($line =~ m/^\s*chr/);
+      next if $line =~ /^\s*chr\tstartpos/;
       my ($chr, $start, $end, $mt_cn_maj, $mt_cn_min, $mt_frac, $mt_cn_maj_sec, $mt_cn_min_sec, $mt_frac_sec) = (split('\s+',$line))[0,1,2,7,8,9,10,11,12];
 
       #Fix to work round instances where the major and minor cn

diff --git a/perl/lib/Sanger/CGP/Battenberg.pm b/perl/lib/Sanger/CGP/Battenberg.pm
@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '3.5.2';
+our $VERSION = '3.5.3';
 our @EXPORT = qw($VERSION);
 
 1;