Version 0.3.1 released

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