bbduk: 'rename' doesn't work if 'mincovfraction' is set
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#49 bbduk: 'rename' doesn't work if 'mincovfraction' is set
It seems using bbduk.sh that the option rename does not work if mincovfraction is set to any value > 0. Referencing the source of the latest release 38.94, the issue appears to happen in the if/else block starting at line 2715 of BBDuk.java. The renaming happens in the function findBestMatch(), and that is only called from within the else block indicated if the condition minCoveredFraction>0 is false.
I'm not entirely sure if this is intended behavior or not, but I don't see why it would be. For now we will have to use minkmerfraction since we need to know which reference sequence was matched.