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

Feature scaliform maven

+ Add scaliform maven plugin
- Removed config for Netbeans, not using the CheckStyle plugin anymore

See merge request !24

Feature sam to fastq

Please merge feature-samTofastq into the develop branch

See merge request !25

Feature extract aligned fastq

This is the tool mentioned in issue #43. In addition to the tool, some notable changes are:

* A new dependency for testing, the [mockito](https://code.google.com/p/mockito/) library, which allows us to mock file system writing so that test times are faster

* Parameterized tests via the `@DataProvider` annotation in testng

* Update to the HTSJDK library usage in GATK 3.3

See merge request !22

Conflicts:
	biopet-framework/BiopetFramework.iml
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala

Feature toolcommands

Added 4 tools from Sage
see also #67

See merge request !19

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