Removing intervals from PrintReads

This causes reads mapped outside of the targeted area to be discarded, which is not the desired behaviour.
Correct java version in setup

Thanks Mårten for reporting this.
Newest gatk version checked out
Changing VC script to reflect GATK changes

Can no longer use PercentBadVariants. So this has been removed.
Changes to the test framework and tests

This is not working right now. The pipeline tests are throwing NoClassDefFound. Will investigate this further.
All tests pass dry run
Changing java module loaded
Changed md5sums to reflect new versions
Working VC tests
New spec is 200 minimum downsampling for HP
Haloplex tests working
RNAQC tests ok
Travis should not build to JVM 1.6

Note that the data processing tests are still failing when actually running them!
All tests passing
Adding flatfile report reader
Automatic switch for xml or tsv report and...

... some general refactoring to make the API names more representative.
Adding discovery of tsv to SetupCreator
Update to README about report.tsv
Adding Olofs filter suggestion on SetupFileCreator

This makes sure that the SetupFileCreator does not fail if there are files in the run folder root dir.
Added missing path_to_samtools variable