Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

Feature vcffilter trio filters

Added some more filter options

See merge request !162

zcat fix for mapping pipeline

This fix makes sure that the pipeline first performs a zcat on gzipped fastq files.

See merge request !161

Fix mpileup to vcf

Fix MpileupToVcf to handle multi-nuclitides char better.

Also some refactoring in mapping and flexiprep. R2 should now be a Option[File], also for #133

See merge request !160

Feature improved bammetrics

see #127

See merge request !158

Fix flag handling and add some logging

See merge request !159

Patch rscript

See merge request !156