org.hammerlab.guacamole

commands

package commands

Commands (such as variant callers) that can be invoked on the command line.

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Type Members

  1. trait Args extends Args4jBase

  2. abstract class Command[T <: Args] extends Serializable with Logging

    Interface for running a command from command line arguments.

  3. class PartitionLociArgs extends Args4jBase with Args with LociPartitionerArgs with HalfWindowArgs with Arguments

  4. class PartitionReadsArgs extends Args4jBase with Args with Arguments with PartitionedRegionsArgs with HalfWindowArgs

  5. abstract class SparkCommand[T <: Args] extends Command[T]

  6. case class VariantLocus(sampleId: SampleId, contigName: ContigName, locus: Locus, variantAlleleFrequency: Float) extends Product with Serializable

    VariantLocus is a locus and the variant allele frequency at that locus

Value Members

  1. object GermlineAssemblyCaller

    Simple assembly based germline variant caller

  2. object PartitionLoci extends SparkCommand[PartitionLociArgs]

  3. object PartitionReads extends SparkCommand[PartitionReadsArgs]

  4. object SomaticJoint

  5. object SomaticStandard

    Simple subtraction based somatic variant caller

  6. object VAFHistogram

  7. object VariantLocus extends Serializable

  8. object VariantSupport

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