Release notes Biopet version 0.5.0

General Code changes

Upgrade to Queue 3.4, with this also the htsjdk library to 1.132
Our QC and Mapping pipeline now use piping for the most used aligners and QC tools
- Reducing I/O over the network
- Reducing the disk usage (storage) and run time
Added version command for Star
Seperation of the biopet-framework into: Core, Extensions, Tools and Utils
Optimized unit testing
Unit test coverage on Tools increased
Workaround: Added R-script files of Picard to biopet to fix picard jobs (files are not packaged in maven dependency)
Added external example for developers

Retries of pipeline and tools is now enabled by default
Improvements in the reporting framework, allowing custom reporting elements for specific pipelines.
Fixed reports when metrics of Flexiprep is skipped
Added metagenomics pipeline: Gears
Added single sample variantcalling with bcftools
Added ET + key support for GATK job invocation, disable phone-home feature when key is supplied
Added more debug information in the .log directory when -l debug is enabled
Shiva: added support for GenotypeConcordance tool to check against a Golden Standard
Shiva: fixed a lot of small bugs when developing integration tests
Shiva: Workaround: Fixed a dependency on rerun, with this change there can be 2 bam files in the samples folder
Gentrap: Improved error handling on missing annotation files