Feature fix logs

Fix for double logs for BiopetQCommandLine

See merge request !42

Feature bump version

see #56

See merge request !40

Feature sharkapps

sample config file, which should be used by everyone during development.

See merge request !41

Feature fix gatk pipeline

Fix some small options on the gatk pipeline

See merge request !39

Feature dirty warns

See #75

See merge request !38

Allele mode now also on discovery alleles

Feature cach version

See #84

See merge request !35

Feature fix deprecation

see #85

See merge request !37

Feature fix sortsam

See #20

See merge request !36

Feature extract fix

Missed a test case which again manifests into a bug where filtering doesn't work for FASTQ files with description lines.

Anyway, this updates the test case and fixes the problem.

EDIT: also fixes bug that arises when supplying multiple intervals.

See merge request !34

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