<commit_before># cgpVAF

| Master                                        | Develop                                         |
| --------------------------------------------- | ----------------------------------------------- |
| [![Master Badge][travis-master-badge]][travis-repo] | [![Develop Badge][travis-develop-badge]][travis-repo] |


<!-- TOC depthFrom:2 depthTo:6 withLinks:1 updateOnSave:1 orderedList:0 -->

- [vafCorrect](#cgpVaf)
- [Quick installation](#quick-installation)
	- [Skipping all external dependencies](#skipping-all-external-dependencies)
	- [Skipping exonerate install](#skipping-exonerate-install)
- [INSTALL](#install)
	- [Dependencies](#package-dependencies)
- [Creating a release](#creating-a-release)
	- [Preparation](#preparation)
	- [Cutting the release](#cutting-the-release)
- [LICENSE](#License)

<!-- /TOC -->

## vafCorrect

Calculates the Variant Allele Fraction for variants sites in VCF and/or BED file 
This script performs comparative analysis of variant sites in multiple tumour/normal samples in an individual.
Also facilitates the merging of varinats sites across the samples in a sample group defined by 
set of related samples in an individual and provides unbiased pileup[MNV] and exonerate[Indel] output for each variant site.

## Quick installation

```
./setup.sh path_to_install_to
```

### Skipping all external dependencies

If you want to only install vafCorrect and use existing versions of
tools from your path run as:

```
./setup.sh path_to_install_to 1
```

### Skipping exonerate install

Central install via package manager of 2.2.0 is adequate. To skip just exonerate install run:

```
./setup.sh path_to_install_to 2
```


## INSTALL 

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

 * [Samtools] ( max 0.1.20 until perl bindings are updated)
 * [vcftools]
 * [Bio-HTS] 
 * [Exonerate]

 `setup.sh` should install these dependencies.  

```
./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 `perl/lib/Sanger/CGP/Vaf.pm` to the correct version.
2. Update `CHANGES.md` to show major items.
3. Run `./perl/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) 2017-2018 Genome Research Ltd.

Author: <NAME> <<EMAIL>>

This file is part of vafCorrect.

vafCorrect 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’."
```

<!-- References -->
[Samtools]: https://github.com/samtools/samtools <commit_msg>[skip travis] Clean up README to explain some tools are always installed, fix licence year<commit_after># cgpVAF

| Master                                        | Develop                                         |
| --------------------------------------------- | ----------------------------------------------- |
| [![Master Badge][travis-master-badge]][travis-repo] | [![Develop Badge][travis-develop-badge]][travis-repo] |

* [vafCorrect](#vafcorrect)
* [Quick installation](#quick-installation)
	* [Skipping all external dependencies](#skipping-all-external-dependencies)
	* [Skipping exonerate install](#skipping-exonerate-install)
* [INSTALL](#install)
	* [Dependencies](#dependencies)
* [Creating a release](#creating-a-release)
	* [Preparation](#preparation)
	* [Cutting the release](#cutting-the-release)
* [LICENCE](#licence)

## vafCorrect

Calculates the Variant Allele Fraction for variants sites in VCF and/or BED file
This script performs comparative analysis of variant sites in multiple tumour/normal samples in an individual.
Also facilitates the merging of varinats sites across the samples in a sample group defined by
set of related samples in an individual and provides unbiased pileup[MNV] and exonerate[Indel] output for each variant site.

## Quick installation

```bash
./setup.sh path_to_install_to
```

### Skipping all external dependencies

If you want to only install vafCorrect and use existing versions of
tools from your path run as:

```bash
./setup.sh path_to_install_to 1
```

`vcftools` and `htslib` still need to install in this instances as they have perl module bindings
which are required dependencies.

### Skipping exonerate install

Central install via package manager of 2.2.0 is adequate. To skip just exonerate install run:

```bash
./setup.sh path_to_install_to 2
```

## INSTALL

### Dependencies

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

* [Samtools]
* [vcftools]
* [Bio-HTS]
* [Exonerate]

`setup.sh` should install these dependencies.

```bash
./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 `perl/lib/Sanger/CGP/Vaf.pm` to the correct version.
2. Update `CHANGES.md` to show major items.
3. Run `./perl/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) 2017-2019 Genome Research Ltd.

Author: CASM/Cancer IT <<EMAIL>>

This file is part of vafCorrect.

vafCorrect 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’."
```

<!-- References -->
[Samtools]: https://github.com/samtools/samtools
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