org.bdgenomics.adam.algorithms.consensus

# ConsensusGenerator

#### abstract class ConsensusGenerator extends Serializable

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ConsensusGeneratorFromKnowns, ConsensusGeneratorFromReads, ConsensusGeneratorFromSmithWaterman
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### Instance Constructors

1. #### new ConsensusGenerator()

### Abstract Value Members

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.g., indel normalization.

   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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