├── .gitignore ├── .travis.yml ├── CHANGES.md ├── Dockerfile ├── LICENSE.TXT ├── README.md ├── Rsupport ├── libInstall.R └── setupR.sh ├── perl ├── MANIFEST ├── MANIFEST.SKIP ├── Makefile.PL ├── bin │ ├── battenberg.pl │ ├── battenberg_CN_to_VCF.pl │ ├── battenberg_version.pl │ ├── bb_vcf_to_ascat_cn.pl │ └── download_generate_bberg_ref_files.pl ├── docs.tar.gz ├── lib │ └── Sanger │ │ └── CGP │ │ ├── Battenberg.pm │ │ └── Battenberg │ │ └── Implement.pm ├── share │ ├── battenberg │ │ └── probloci.txt.gz │ └── gender │ │ └── GRCh37d5_Y.loci └── t │ ├── 1_pm_compile.t │ └── 2_pl_compile.t ├── prerelease.sh └── setup.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cancerit/cgpBattenberg/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 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