Start on window based structural variant caller

This is a basic structural variant caller based on simple paired-end alignment rules.

It it currently fairly overagressive in calling variants, but should pick up on most simple ones.  I haven't been able to evalaute it on the synthetic sets yet, as we need to improve our VCF output to do so (need to output SVLEN, SVEND and different types of SVs, etc, will open an issue)