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.
- Alphabetic
- By Inheritance
- ConsensusGenerator
- Serializable
- Serializable
- AnyRef
- Any
- Hide All
- Show All
- Public
- All
Instance Constructors
- new ConsensusGenerator()
Abstract Value Members
-
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.
-
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.
-
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
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
clone(): AnyRef
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native() @HotSpotIntrinsicCandidate()
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native() @HotSpotIntrinsicCandidate()
-
def
numAlignmentBlocks(cigar: Cigar): Int
- cigar
The CIGAR to process.
- returns
The number of alignment blocks that are alignment matches.
- Attributes
- protected
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toString(): String
- Definition Classes
- AnyRef → Any
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
Deprecated Value Members
-
def
finalize(): Unit
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] ) @Deprecated
- Deprecated