Merge branch 'feature-extract_aligned_fastq' into 'develop'

Feature extract aligned fastq

This is the tool mentioned in issue #43. In addition to the tool, some notable changes are:

* A new dependency for testing, the [mockito](https://code.google.com/p/mockito/) library, which allows us to mock file system writing so that test times are faster

* Parameterized tests via the `@DataProvider` annotation in testng

* Update to the HTSJDK library usage in GATK 3.3

See merge request !22