org.broadinstitute.hellbender.utils.read.mergealignment

Class BestEndMapqPrimaryAlignmentStrategy

java.lang.Object

org.broadinstitute.hellbender.utils.read.mergealignment.BestEndMapqPrimaryAlignmentStrategy

All Implemented Interfaces:

PrimaryAlignmentSelectionStrategy

public final class BestEndMapqPrimaryAlignmentStrategy
extends java.lang.Object
implements PrimaryAlignmentSelectionStrategy

For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary. The primary alignments are then correlated so that their mate info points to each other, but all non-primary alignments are uncorrelated.

Constructor Summary

Constructors

Constructor and Description
BestEndMapqPrimaryAlignmentStrategy()

Method Summary

Modifier and Type	Method and Description
void	pickPrimaryAlignment(HitsForInsert hits) Primary alignment was filtered out.

Methods inherited from class java.lang.Object

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

Constructor Detail

BestEndMapqPrimaryAlignmentStrategy

public BestEndMapqPrimaryAlignmentStrategy()

Method Detail

pickPrimaryAlignment

public void pickPrimaryAlignment(HitsForInsert hits)

Primary alignment was filtered out. Need to select a new one.

Specified by:

pickPrimaryAlignment in interface PrimaryAlignmentSelectionStrategy