org.broadinstitute.hellbender.tools.spark.sv.evidence

Class FermiLiteAssemblyHandler

java.lang.Object

org.broadinstitute.hellbender.tools.spark.sv.evidence.FermiLiteAssemblyHandler

public final class FermiLiteAssemblyHandler
extends java.lang.Object

LocalAssemblyHandler that uses FermiLite.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
FermiLiteAssemblyHandler(java.lang.String alignerIndexFile, int maxFastqSize, java.lang.String fastqDir, boolean writeGFAs, boolean popVariantBubbles, boolean removeShadowedContigs, boolean expandAssemblyGraph, int zDropoff)

Method Summary

Modifier and Type	Method and Description
AlignedAssemblyOrExcuse	apply(scala.Tuple2<java.lang.Integer,java.util.List<SVFastqUtils.FastqRead>> intervalAndReads) This method creates an assembly with FermiLite, and uses the graph information returned by that assembler to stitch together valid paths through the contigs.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.util.function.Function

andThen, compose, identity

Constructor Detail

FermiLiteAssemblyHandler

public FermiLiteAssemblyHandler(java.lang.String alignerIndexFile,
                                int maxFastqSize,
                                java.lang.String fastqDir,
                                boolean writeGFAs,
                                boolean popVariantBubbles,
                                boolean removeShadowedContigs,
                                boolean expandAssemblyGraph,
                                int zDropoff)

Method Detail

apply

public AlignedAssemblyOrExcuse apply(scala.Tuple2<java.lang.Integer,java.util.List<SVFastqUtils.FastqRead>> intervalAndReads)

This method creates an assembly with FermiLite, and uses the graph information returned by that assembler to stitch together valid paths through the contigs. These paths are then aligned to reference with BWA.