3.5.3 - GRCh38 specific bugfix

Fix to file conversion step which resulted in empty files for:

• battenberg.tum.cn.bed
• battenberg.summary.csv
• battenberg.norm.cn.bed

3.5.0 - GRCh38 Ready

GRCh38 users: please see/update to 3.5.3

• Changes required for use with GRCh38 compatible Battenberg R
• some reference files 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

v3.3.1- minor bugfix release

• 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

Update R libs

Updates core versions of battenberg-R and ASCAT-R code

v3.2.2 - minor bugfix release

• Updates to documentation
• Added extra information to the README

Feature - v3.2.0 - Install Battenberg R code from GitHub

• Automatic installation of Battenberg R code v2.2.5 from GitHub

Feature - v3.1.0 - New dense snps alleleCounter version

• New dense snps alleleCounter version

v3.0.2 - minor bugfix release

• Fix to avoid glob bug in perl 5.16.3

v3.0.1 - minor bugfix release

• Bug fix to bb_vcf_to_ascat_cn.pl which crashed when there were regions which had no copynumber values set

Feature Release - 3.0.0

• Uses version 2.2.5 of the battenberg R package
• Removed R files from repository