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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 calledarithmeanqual
and can be used in the following fashion:bioawk -c fastx '{print arithmeanqual($qual)}' mydata.fastq
Thanks!