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FASTQ average quality score calculation can be faster #28

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rhpvorderman opened this issue Mar 24, 2023 · 2 comments
Closed

FASTQ average quality score calculation can be faster #28

rhpvorderman opened this issue Mar 24, 2023 · 2 comments

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@rhpvorderman
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See nanoporetech/bonito#336

Also thanks for your post on https://gigabaseorgigabyte.wordpress.com/2017/06/26/averaging-basecall-quality-scores-the-right-way/ it was tremendously helpful.
Unfortunately a lot of tools still do it wrong. Even FastQC(!).

@wdecoster
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Isn't what you suggest implemented here?
I believe the function errs_tab() is executed only once when ave_qual() is initialized (credits go to @bsipos for wdecoster/nanomath#13).

@rhpvorderman
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Whoops. Looks like I completely misread your code. In that case, I am sorry to have bothered you!

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