Change defaults in 3.0

[NickSto]

Version 3.0 offers an opportunity to change some default settings. Let's list them here.

make-consensi.py

--aligner: biopython Currently it's swalign, an esoteric Smith Waterman implementation. That'll require BioPython as a dependency, though. - Ideally version 1.75 at least --cons-thres: 0.7 Currently set to 0.5, but it should default to the threshold recommended by the duplex sequencing designers in Kennedy et al. 2014 (page 4).

correct.py

--dist: 3 Currently it's 1, but a more aggressive setting is still pretty safe. I've already changed the default in the Galaxy tool.

[NickSto]

Re-opening with the addition of --cons-thres to the list.