I will update the description; it's a bit misleading. What it means is, reads with average quality below the setting will not be mapped. All of the reads will still be printed to "out", even if they failed the quality threshold. However, if you use the "outm" and "outu" streams, only mapped reads will go to outm, and only unmapped reads will go to outu. So, maq would suppress low-quality reads from going to outm.
Thanks for noting that the long version of the flag does not work. It's actually "minavgquality"; I'll fix that.
Thanks for noting that the long version of the flag does not work. It's actually "minavgquality"; I'll fix that.
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