Class/Object

org.bdgenomics.adam.algorithms.consensus

ConsensusGenerator

Related Docs: object ConsensusGenerator | package consensus

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abstract class ConsensusGenerator extends Serializable

Abstract class for generating consensus sequences for INDEL realignment.

INDEL realignment scores read alignments against the reference genome and a set of "consensus" sequences. These consensus sequences represent alternate alleles/haplotypes, and can be generated via a variety of methods (e.g., seen in previous projects --> 1kg INDELs, seen in read alignments, etc). This trait provides an interface that a consensus generation method should implement to provide it's consensus sequences to the realigner.

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Instance Constructors

  1. new ConsensusGenerator()

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Abstract Value Members

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

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    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[RichAlignment], reference: String, region: ReferenceRegion): Iterable[RichAlignment]

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

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

    reads

    Reads to preprocess.

    reference

    Reference genome bases covering this target.

    region

    The region covered by this target.

    returns

    Preprocessed reads.

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

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    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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  15. def numAlignmentBlocks(cigar: Cigar): Int

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    cigar

    The CIGAR to process.

    returns

    The number of alignment blocks that are alignment matches.

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

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