cgpVcf

cgpVcf contains a set of common perl utilities for generating consistent Vcf headers.

It primarily exists to prevent code duplication between some other projects.

Master	Dev

---

Dependencies/Install

Some of the code included in this package has dependencies on several C packages:

• samtools v1.2+
• vcftools

And various perl modules.

Please use setup.sh to install the dependencies. Setting the environment variable CGP_PERLLIBS allows you to to append to PERL5LIB during install. Without this all dependancies are installed into the target area.

Please be aware that this expects basic C compilation libraries and tools to be available.

---

Creating a release

Preparation

• Commit/push all relevant changes.
• Pull a clean version of the repo and use this for the following steps.

Cutting the release

1. Update lib/Sanger/CGP/Vcf.pm to the correct version (adding rc/beta to end if applicable).
2. Update CHANGES.md to show major items.
3. Run ./prerelease.sh
4. Check all tests and coverage reports are acceptable.
5. Commit the updated docs tree and updated module/version.
6. Push commits.
7. Use the GitHub tools to draft a release.

LICENCE

Copyright (c) 2014-2018 Genome Research Ltd.

Author: Cancer Genome Project <cgpit@sanger.ac.uk>

This file is part of cgpVcf.

cgpVcf is free software: you can redistribute it and/or modify it under
the terms of the GNU Affero General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option) any
later version.

This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
details.

You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.

1. The usage of a range of years within a copyright statement contained within
this distribution should be interpreted as being equivalent to a list of years
including the first and last year specified and all consecutive years between
them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007-
2009, 2011-2012’ should be interpreted as being identical to a statement that
reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright
statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being
identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
2009, 2010, 2011, 2012’."