bioawk
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Add arithmetic meanqual
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!
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