org.bdgenomics.adam.algorithms.consensus

ConsensusGenerator

abstract class ConsensusGenerator extends Serializable

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  1. new ConsensusGenerator()

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  1. abstract def findConsensus(reads: Iterable[RichAlignmentRecord]): Iterable[Consensus]

    For all reads in this region, generates the list of consensus sequences for realignment.

    For all reads in this region, generates the list of consensus sequences for realignment.

    reads

    Reads to generate consensus sequences from.

    returns

    Consensus sequences to use for realignment.

  2. abstract def preprocessReadsForRealignment(reads: Iterable[RichAlignmentRecord], reference: String, region: ReferenceRegion): Iterable[RichAlignmentRecord]

    Performs any preprocessing specific to this consensus generation algorithm, e.

    Performs any preprocessing specific to this consensus generation algorithm, e.g., indel normalization.

    reads

    Reads to preprocess.

    returns

    Preprocessed reads.

  3. abstract def targetsToAdd(): Option[RDD[IndelRealignmentTarget]]

    Generates targets to add to initial set of indel realignment targets, if additional targets are necessary.

    Generates targets to add to initial set of indel realignment targets, if additional targets are necessary.

    returns

    Returns an option which wraps an RDD of indel realignment targets.

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