Feature dirty warns

See #75

See merge request !38

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

Feature raxml extension

See #80

See merge request !31

config, issue #82

Feature pom updates

See commits :).

See merge request !29