Feature wipereads (final)

Now we have simple GTF +refFlat support, with more tests + some cleanup :).

The feature branch can be deleted afterwards.

See merge request !33

Feature xml dependency fix

See commits :) ~ we've been packaging 2 dependencies that are required only for testing in our JAR files. This should fix that.

See merge request !32

Feature varianteval

for ticket #82 , Queue wrapper around the GATK class..

See merge request !30

Feature raxml extension

See #80

See merge request !31

config, issue #82

Feature pom updates

See commits :).

See merge request !29

Feature ln fix

@w.arindrarto , could you check this first?

the ' single-quotes are giving me trouble in executing as a InProgressFunction.

See merge request !26

Feature wipereads enhancements + quicker testing

Lots of internal refactors (mainly because of GATK 3.3 updates, but also to reduce code repetition by using more of `htsjdk`'s already defined functions).

Also, no more `null`s and testing is now faster :face_with_look_of_triumph: !

See merge request !27

Feature extract aligned fastq

This fixes the bug found earlier (unreported) in command line invocation. Also, tests are now done on the command line flag (which comes with the required refactoring).

See merge request !28

Conflicts:
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala