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ctSkennerton
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May 22, 2019
Fix initial "fields" buffer size
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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? |
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I added a function that calculates the arithmetic mean of the quality scores, rather than the geometric mean as
meanqualcurrently 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
bioawkmethod is calledarithmeanqualand can be used in the following fashion:bioawk -c fastx '{print arithmeanqual($qual)}' mydata.fastqThanks!