org.bdgenomics.adam.algorithms.consensus

# ConsensusGenerator

#### trait ConsensusGenerator extends Serializable

Trait 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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### 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.

   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]]

   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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17. #### def numAlignmentBlocks(cigar: Cigar): Int

    cigar

      The CIGAR to process.

    returns

      The number of alignment blocks that are alignment matches.

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