Generalise default and per sample specification of parameters

[timothymillar]

Currently there are a number of parameters that may be specified globally or on a per sample basis (using the global value as a default). This is a general pattern for specifying parameters and is only going to increase. Additionally it would be useful to specify different values based on genomic locus (ala freebayes).

Handling each case individually is verbose and error prone so it would be good to establish a generic approach to handling parameters on a default, per-sample and per-locus bases (i.e. a parameter matrix). It is probably worth investigating alternatives to argparse as part of this.