Add arguments. Fix coverage calculation. The first fix create new problems with overlapping alignments, which is fixed in this version.
0.1.3
Update argument structure.
0.1.2
Fix problem with ORF-HMM alignments which were split across multiple lines in the HMMER output. Prior to this version only the best match was chosen, now coverage is summed across the domain alignments, solving problems with detection of fusion proteins
0.1.1
Input can now be a prodigal-formatted protein fasta, by adding the `--aa` argument