Optionally output the raw alignment score, not just the bit score

[torognes]

The raw alignment scores are not shown unless including alignments in the default output format. An option to include the raw alignment scores will be useful in some cases.

[odoublewen]

I found this issue after getting confused about the --min_score option:

  -c, --min_score=NUM        minimum score of sequences to show (1)

I assumed this referred to the bit score, since I was working with tabular output. It would be nice to clarify in the usage that this is the raw, not bit, score.

And thanks for the great aligner!!!

[torognes]

I assumed this referred to the bit score, since I was working with tabular output. It would be nice to clarify in the usage that this is the raw, not bit, score.

Thanks for your comment. I have clarified this in the README file now.