Version 0.3.1 released

We've just released version 0.3.1. The most visible changes are (i) LoFreq's output is now chromosome aware (an overdue feature), (ii) the Samtools pileup is now generated internally (no more messing with samtools by the user needed), (iii) the added support for region bed files (which allows to restrict the analysis to regions) and (iv) the addition of the LoFreq unique pipeline script (for e.g. easy somatic snv calls) and a couple more helper scripts.