Copyright (c) 2014 Genome Research Ltd.

Author: CancerIT cgpit@sanger.ac.uk

This file is part of alleleCount.

alleleCount 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’."

The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenburg.

All that this contains is a perl program to calculate the allele fraction for locations provided in an input file.

The C version of bam_stats supports both BAM and CRAM input.

###Dependencies/Install Some of the code included in this package has dependencies on several C packages:

• samtools v0.1.20, via Bio::DB::Sam
• htslib

And various utility perl modules.

(samtools is only required for legacy perl version of bam_stats.pl and will be removed at a later date).

Once complete please run:

./setup.sh /some/install/location

Please be aware that this expects basic C compilation libraries and tools to be available, most are listed in INSTALL.

##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/AlleleCount.pm to the correct version (adding rc/beta to end if applicable).
2. Update c/Makefile to contain the correct version.
3. Update Changes to show major items.
4. Run ./prerelease.sh
5. Check all tests and coverage reports are acceptable.
6. Commit the updated docs tree and updated module/version.
7. Push commits.
8. Use the GitHub tools to draft a release.