org.hammerlab.genomics

readsets

package readsets

This package contains functionality related to processing multiple "sets of reads" (e.g. BAM files) in the context of a single analysis.

For example, a standard somatic caller will typically load and analyze separate "normal" and "tumor" samples, each corresponding to an RDD[MappedRead], but which will also share metadata, like the org.hammerlab.genomics.reference.ContigName of the reference they are mapped to.

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Type Members

  1. trait HasSampleId extends Any

  2. type NumSamples = Int

  3. type PerSample[+A] = IndexedSeq[A]

  4. case class ReadSets(readsRDDs: PerSample[ReadsRDD], sequenceDictionary: SequenceDictionary, contigLengths: ContigLengths) extends PerSample[ReadsRDD] with Product with Serializable

    A ReadSets contains reads from multiple inputs as well as SequenceDictionary / contig-length information merged from them.

  5. class Registrar extends KryoRegistrator

  6. type SampleId = Int

  7. type SampleName = String

  8. implicit final class SampleRead extends AnyVal with HasSampleId

  9. type SampleRegion = Region with HasSampleId

Value Members

  1. object ReadSets extends Logging with Serializable

  2. object SampleRead

  3. package args

  4. package io

  5. package rdd

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