On 7/11/14, 9:19 AM, Kanterakis, Efstathios wrote:
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
Hi Stathis,
This is a bug in the code that generates the usage message. MQ is
required, as you discovered.
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?
Does CollectAlignmentSummaryMetrics not provide the information you need?
-Alec
Thank you very much.
Stathis
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