Update server
Merge develop
Update run script. Fixes issue #42
Update docs. Add examples, clean-up README
Update docs
Add docs on pypi and installation quirks
Make sure bam file list is unique
Fixes issue #45
Merge remote branch 'origin/master'
Fix error in CombineVariants - splitting always done on one chromosome
Add VALIDATION_STRINGENCY to picard
Add VALIDATION_STRINGENCY to all picard tasks
Add basic support for ratatosk.log
Make all modules use ratatosk log interface
Add ratatosk.lib.files.input and add base classes for input files
Remove SnpEffWrapper - VariantSnpEffAnnotator requires two vcf files
Add support for genotyping at alleles
Add CombineVariants and CombineSplitVariants
Add Sample abc class
Make target generator functions use ratatosk.experiment.ISample