Value Members
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==(arg0: Any): Boolean
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apply(cmdLine: Array[String]): ADAMCommand
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asInstanceOf[T0]: T0
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notifyAll(): Unit
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toString(): String
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wait(): Unit
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wait(arg0: Long, arg1: Int): Unit
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Inherited from AnyRef
Inherited from Any
CalculateDepth (accessible as the command 'depth' through the CLI) takes two arguments, an Read file and a VCF (or equivalent) file, and calculates the number of reads (the 'depth') from the Read file which overlap each of the variants given by the VCF. It then reports, on standard out, the location and name of each variant along with the calculated depth.