Merge branch 'release/3.5.0'

Author: David Jones

CHANGES.md

@@ -1,16 +1,23 @@
 # Changes
 
+## 3.5.0
+
+* Changes required for use with GRCh38 compatible Battenberg R
+* **some reference files for for chromosome X will require renaming in GRCh37**
+* `mv 1000_genomes_GC_corr_chr_23.txt.gz 1000_genomes_GC_corr_chr_X.txt.gz`
+* `mv 1000genomesAlleles2012_chr23.txt 1000genomesAlleles2012_chrX.txt`
+* `mv 1000genomesloci2012_chr23.txt 1000genomesloci2012_chrX.txt`
+* This release points to cancerit fork of core battenberg algorithm [here](https://github.com/cancerit/battenberg/feature/grch38)
+
 ## 3.4.0
 
 * Placed into a container.
 
-
 ## 3.3.1
 
 * Fixed bug when creating split loci files which would occasionally count wrongly due to rounding errors. Fixed the cause of the rounding error and added a sort to the hash.
 * Added check that the number of split loci files is at least the number of required contigs
 
-
 ## 3.3.0
 
 * Upgrade to Battenberg [v2.2.8](https://github.com/Wedge-Oxford/battenberg/releases/tag/v2.2.8).

README.md

@@ -84,16 +84,17 @@ Some required data files are not included in the distribution but a script is in
   * Included: ``files/probloci.txt.gz``
 
 Additionally, the wgs_gc_correction_1000g files need to be downloaded. These can be obtained from the Battenberg R code site [here][bb-ref].
+  * The chr X wgs_gc_correction_1000g will require renaming. `mv 1000_genomes_GC_corr_chr_23.txt.gz 1000_genomes_GC_corr_chr_X.txt.gz` 
 
 ## Program Run Instructions
 
 For the most up to date usage instructions for the wrapper code please see the command line help:
 
-    battenberg.pl -h
+`battenberg.pl -h`
 
 Please check the [wiki][cgpbb-wiki] for common problems before raising any issues.
 
-# LICENCE
+## LICENCE
 
 ```
 Copyright (c) 2014-2018 Genome Research Ltd.

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='v2.2.8' # with 'v', this is a project archive
+VERSION_BB='v2.3.0' # with 'v', this is a project archive
 
 CPU=`grep -c ^processor /proc/cpuinfo`
 if [ $? -eq 0 ]; then
@@ -85,7 +85,7 @@ if [ "x$BUILD_R" != "x" ]; then
 fi
 
 curl -sSL https://github.com/Crick-CancerGenomics/ascat/releases/download/v${VERSION_ASCAT}/ASCAT_${VERSION_ASCAT}.tar.gz > ascat_R.tar.gz
-curl -sSL https://github.com/Wedge-Oxford/battenberg/archive/$VERSION_BB.tar.gz > BB_R.tar.gz
+curl -sSL https://github.com/cancerit/battenberg/archive/$VERSION_BB.tar.gz > BB_R.tar.gz
 
 Rscript $INIT_DIR/libInstall.R $R_LIBS_USER ascat_R.tar.gz BB_R.tar.gz 2>&1 | grep '^\*'
 

perl/bin/battenberg.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2019 Genome Research Ltd.
 #
 # Author: Cancer Genome Project <cgphelp@sanger.ac.uk>
 #
@@ -283,8 +283,9 @@ sub setup {
   }
   PCAP::Cli::file_for_reading('reference',$opts{'reference'});
 
-  my $no_of_jobs = Sanger::CGP::Battenberg::Implement::file_line_count_with_ignore($opts{'reference'},$opts{'ignored_contigs'});
+  my ($no_of_jobs, $contig_list) = Sanger::CGP::Battenberg::Implement::file_line_count_with_ignore($opts{'reference'},$opts{'ignored_contigs'});
   $opts{'job_count'} = $no_of_jobs;
+  $opts{'contig_list'} = $contig_list;
 
   #Set number of loci files to be the number of chromosomes if not set
   my $loci_files_defined = 1;

perl/bin/battenberg_CN_to_VCF.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2019 Genome Research Ltd.
 #
 # Author: David Jones <cgphelp@sanger.ac.uk>
 #

perl/bin/battenberg_version.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2019 Genome Research Ltd.
 #
 # Author: Cancer Genome Project <cgphelp@sanger.ac.uk>
 #

perl/bin/bb_vcf_to_ascat_cn.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl
 
 ##########LICENCE##########
-# Copyright (c) 2014-2018 Genome Research Ltd.
+# Copyright (c) 2014-2019 Genome Research Ltd.
 #
 # Author: David Jones <cgphelp@sanger.ac.uk>
 #