ADAM_2.12: Core 0.30.0 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package algorithms
  Definition Classes
    adam
-  package consensus
  Definition Classes
    algorithms
- ConsensusGenerator

c

org.bdgenomics.adam.algorithms.consensus

# ConsensusGenerator 

###
Companion object ConsensusGenerator

#### 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.

Linear Supertypes
Serializable, Serializable, AnyRef, Any
 
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. ConsensusGenerator
2. Serializable
3. Serializable
4. AnyRef
5. Any

1. Hide All
2. Show All

Visibility

1. Public
2. All

### Instance Constructors

1.  new ConsensusGenerator()

### Abstract Value Members

1.  abstract def findConsensus(reads: Iterable[RichAlignment]): 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[RichAlignment], reference: String, region: ReferenceRegion): Iterable[RichAlignment]

   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]]

   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.

### Concrete Value Members

1.  final def !=(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
2.  final def ##(): Int
   Definition Classes
     AnyRef → Any
3.  final def ==(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
4.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
5.  def clone(): AnyRef
   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @native() @throws( ... )
6.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
7.  def equals(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
8.  def finalize(): Unit
   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] )
9.  final def getClass(): Class[_]
   Definition Classes
     AnyRef → Any
   Annotations
     @native()
10.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
11.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
12.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
13.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
14.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
15.  def numAlignmentBlocks(cigar: Cigar): Int

    cigar

      The CIGAR to process.

    returns

      The number of alignment blocks that are alignment matches.

    Attributes
      protected
16.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
17.  def toString(): String
    Definition Classes
      AnyRef → Any
18.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
19.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
20.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @throws( ... )

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped