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torognes / swipe

Smith-Waterman database searches with inter-sequence SIMD parallelisation
GNU Affero General Public License v3.0
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Optionally output the raw alignment score, not just the bit score #11

Open torognes opened 10 years ago

torognes commented 10 years ago

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 commented 4 years ago

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 commented 4 years ago

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.