Make BAM Filtering input parameters less complex.

[jfy133]

Currently there are two logical flags relating to performing samtools filter, one to turn it on (and this assumes for mapQuality filtering) and then an additional to do something with unmapped reads.

From a user perspective this is a little confusing and users may forget to turn on the second flag when they specify how to remove the unmspped reads.

I suggest to remove the second flag and just have an option to do nothing to the unmapped reads (e.g. keep) to skip that functionality