Feature breakdancer

Breakdancer tool is now "feature complete", including the conversion to vcf.

Optimalisation can be scheduled to the next milestone.

See merge request !23

Feature wipereads

The main update here is to use `com.google.guava` for BloomFilter as it works fine with OpenJDK7 (the one that GATK uses internally). This means the pom.xml file has also been updated. As this is mainly for GATK 3.3 dependency, I've also updated the IntelliJ project file.

See merge request !21

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

Feature gatk 3.3

See issue #76

See merge request !20

Feature toolcommands

See merge request !18

Feature metrics on bam input

Added metrics when pipeline starts with bamfile

See merge request !16

Add IntelliJ project files

Two commits here:

* Adding IntelliJ project files (so anybody else could still use IntelliJ ;) + we have the Netbeans configs after all)
* .gitignore update to exclude personal IntelliJ project files

See merge request !15

Feature version

Fix for #10

See merge request !13

Waiyi

merge for ticket #54

See merge request !12

Sander

for #54 and #40

See merge request !11

Bow

Per #54

See merge request !10