Molmed/piper — pull request #2 by johandahlberg (2013-11-21 15:52:56+00:00)
Title: Release v1.1.1 - "Boomer"

**Major changes**

* Changed to the most recent GATK version (2.7-5-g49de937), though this is at the moment checked out from a fork of the GATK (https://github.com/johandahlberg/gatk-protected) as the "jobRunnerJobName" patch (see below) has not been applied to the main GATK branch yet. Later this should be moved back the the main GATK repository.
* The DRMAA job runner now supports the "jobRunnerJobName" field to set the name of the job in the queue. This will hopefully make it easier to handle log parsing in the future. For most jobs it should be set the to something along the lines of `projectName + "_my_awesome_job"`, to make it easier to differentiate between projects in the job queue.
* A tsv format has been provided as an alternative to the report xml's to make it easier to setup Piper with data generated outside the SNP&SEQ Technology platform.
* The script to merge by sample names now hard links files for samples which occur only once.

**Bug fixes**
* Fixing Travis CI problems with running tests.
* Removing intervals from PrintReads, which caused reads mapped outside of the target area to be dropped.
* Correct Java version in setup
* Lots of small bug fixes