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Add arithmetic meanqual

Open conchoecia opened this issue 6 years ago • 1 comments

I added a function that calculates the arithmetic mean of the quality scores, rather than the geometric mean as meanqual currently does.

For motivation, please see this blog post. Using the geometric mean of Q-scores inflates the estimation of the quality of the scores.

The new bioawk method is called arithmeanqual and can be used in the following fashion:

bioawk -c fastx '{print arithmeanqual($qual)}' mydata.fastq

Thanks!

conchoecia avatar Oct 18 '17 06:10 conchoecia

I observe that the meanqual obtained now is not correct for ONT fastq data (far higher than the real value). Could this extra function be merged please to see if it helps or is the meanqual function wrong? Thanks

splaisan avatar Jan 05 '24 09:01 splaisan