Add module for Pilon variant caller

[tseemann]

This is a placeholder to try the Pilon caller - it take standard BAM.

https://github.com/broadinstitute/pilon

[alexjironkin]

Cool, checkout: http://phenix.readthedocs.org/en/latest/api/phe.variant.html#implementing-variant on adding a variant caller. Drop it into phe/variants directory and it will be automatically detected by the system. See http://phenix.readthedocs.org/en/latest/api/phe.variant.html#phe.variant.VariantCaller.make_vcf for the available parameters.