Hello,
Even though the usage message states "This option can be set to 'null' to clear
the default value", when I run Picard (v1.115) CollectWgsMetrics.jar with
MQ=null, I get
java.lang.IllegalArgumentException: Can not set int field
picard.analysis.CollectWgsMetrics.MINIMUM_MAPPING_QUALITY to null value
same for CAP=null
I tried setting MQ=-1 which worked, but CAP=-1 gave me an
java.lang.ArrayIndexOutOfBoundsException: -1
In the end I ran with MQ=-1, CAP=100000
And a feature request, would it be possible to report the number of mapped and
unmapped bases so that one could calculate the number of bases remaining after
filters?
Thank you very much.
Stathis
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