Samtools

[necrolyte2]

from a while back

[averagehat]

This is #72. It can be merged. Not using it right now, but may come into use later, see #66.
Also it includes a fix for vcfcat.

[necrolyte2]

I think the code needs to be restructured and all the assert statements should be pulled out and put into tests file

[averagehat]

Agreed. This is a bit of a mess, I'll do that as I fix the merge conflicts.