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help with scala script and SplitNCigarReads
I'm having some trouble getting the arguments to work properly for SplitNCigarReads in a scala script that are specified in article #3891. Specifically:
-rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 and
What I'm trying is something like:
val SNCR = new SplitNCigarReads with CommonArguments SNCR.input_file :+= qscript.bamFile SNCR.out = swapExt(qscript.bamFile, "bam", "split.bam") SNCR.read_filter :+= "ReassignOneMappingQuality -RMQF 255 -RMQT -60" SNCR.unsafe = "ALLOW_N_CIGAR_READS"
The SNCR.unsafe yields a result that indicates:
found : String("ALLOW_N_CIGAR_READS")
and the SNCR.read_filter will work in the dry run, but when I add the -run flag to my scala script it tells me that this argument isn't valid either.
Any thoughts from some scala pros?