org.bdgenomics.adam.rdd

ADAMRodRDDFunctions

class ADAMRodRDDFunctions extends Serializable with Logging

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Instance Constructors

  1. new ADAMRodRDDFunctions(rdd: RDD[ADAMRod])

Value Members

  1. final def !=(arg0: AnyRef): Boolean

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  6. def adamAggregateRods(): RDD[ADAMRod]

    Inside of a rod, aggregates pileup bases together.

    Inside of a rod, aggregates pileup bases together.

    returns

    RDD with aggregated rods.

    See also

    ADAMPileupRDDFunctions#adamAggregatePileups

  7. def adamDivideRodsBySamples(): RDD[(ReferencePosition, List[ADAMRod])]

    Given an RDD of rods, splits the rods up by the specific sample they correspond to.

    Given an RDD of rods, splits the rods up by the specific sample they correspond to. Returns an RDD where the samples are grouped by the reference position.

    returns

    Rods split up by samples and grouped together by position.

  8. def adamRodCoverage(): Double

    Returns the average coverage for all pileups.

    Returns the average coverage for all pileups.

    returns

    Average coverage across mapped loci.

    Note

    If running on an RDD with multiple samples where the rods have been split by sample, will return the average coverage per sample, _averaged_ over all samples. If the RDD contains multiple samples and the rods have _not_ been split, this will return the average coverage per sample, _summed_ over all samples.

    ,

    Coverage value does not include locus positions where no reads are mapped, as no rods exist for these positions.

  9. def adamSplitRodsBySamples(): RDD[ADAMRod]

    Given an RDD of rods, splits the rods up by the specific sample they correspond to.

    Given an RDD of rods, splits the rods up by the specific sample they correspond to. Returns a flat RDD.

    returns

    Rods split up by samples and _not_ grouped together.

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