PileupFlatMapUtils

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17. def pileupFlatMapMultipleSamples[T](sampleNames: PerSample[SampleName], partitionedReads: PartitionedReads, skipEmpty: Boolean, function: (PerSample[Pileup]) ⇒ Iterator[T], reference: ReferenceGenome)(implicit arg0: ClassTag[T]): RDD[T]

    Flatmap across loci and any number of RDDs of MappedReads.

    Flatmap across loci and any number of RDDs of MappedReads.

    See also

    the splitSamplesAndMap function for other argument descriptions.

18. def pileupFlatMapOneSample[T](partitionedReads: PartitionedReads, sampleName: SampleName, skipEmpty: Boolean, function: (Pileup) ⇒ Iterator[T], reference: ReferenceGenome)(implicit arg0: ClassTag[T]): RDD[T]

    Flatmap across loci, where at each locus the provided function is passed a Pileup instance.

    Flatmap across loci, where at each locus the provided function is passed a Pileup instance.

    skipEmpty

    If true, the function will only be called at loci that have nonempty pileups, i.e. those where at least one read overlaps. If false, then the function will be called at all the specified loci. In cases where whole contigs may have no reads mapped (e.g. if running on only a single chromosome, but loading loci from a sequence dictionary that includes the entire genome), this is an important optimization.

    See also

    the splitSamplesAndMap function for other argument descriptions

19. def pileupFlatMapTwoSamples[T](partitionedReads: PartitionedReads, sample1Name: SampleName, sample2Name: SampleName, skipEmpty: Boolean, function: (Pileup, Pileup) ⇒ Iterator[T], reference: ReferenceGenome)(implicit arg0: ClassTag[T]): RDD[T]

    Flatmap across loci on two RDDs of MappedReads.

    Flatmap across loci on two RDDs of MappedReads. At each locus the provided function is passed two Pileup instances, giving the pileup for the reads in each RDD at that locus.

    skipEmpty

    see pileupFlatMapOneSample for description.

    See also

    the splitSamplesAndMap function for other argument descriptions.

20. final def synchronized[T0](arg0: ⇒ T0): T0

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