Another update for Du Novo

Make compiler in Makefile configurable.

Update for Du Novo

Fix compile issue with swalign.h.

Python 3 trimmer.py

Mainly releasing this so Du Novo can use a Python 3 version of trimmer.py.

getreads.py and alignview.py improvements

getreads.py

Parse quality scores, add "lines" format.
Detect incomplete quality score lines.
Don't strip whitespace.
Allow empty sequences.
Add flexibility to "tsv" format.

alignview.py

Filter by quality score.
Add --cons-thres.
Add "msa" format.

trimmer.py

Add paired-end stats.
Set default --min-length to 1.

readsfq.c

Add fast FASTQ counting tool.

Parsers and `trimmer.py`

Improvements to the interface and parsers in getreads.py, an overhaul of alignview.py, and improvements to the statistics reported by trimmer.py.

Releasing to allow inclusion into other projects

This is mainly to give a url to a tarball that can be fetched from platforms like Galaxy and conda.