picard.sam

Class MostDistantPrimaryAlignmentSelectionStrategy

java.lang.Object

picard.sam.MostDistantPrimaryAlignmentSelectionStrategy

All Implemented Interfaces:

PrimaryAlignmentSelectionStrategy

public class MostDistantPrimaryAlignmentSelectionStrategy
extends java.lang.Object
implements PrimaryAlignmentSelectionStrategy

For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size. If such a pair of alignments cannot be found, either because one end is not aligned, or because all alignment pairs are chimeric, then select the best MAPQ for each end independently. 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
MostDistantPrimaryAlignmentSelectionStrategy()

Method Summary

Modifier and Type	Method and Description
void	pickPrimaryAlignment(picard.sam.HitsForInsert hitsForInsert) When this method returns, one alignment has been marked as primary according to the implementation's strategy.

Methods inherited from class java.lang.Object

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

Constructor Detail

MostDistantPrimaryAlignmentSelectionStrategy

public MostDistantPrimaryAlignmentSelectionStrategy()

Method Detail

pickPrimaryAlignment

public void pickPrimaryAlignment(picard.sam.HitsForInsert hitsForInsert)

Description copied from interface: PrimaryAlignmentSelectionStrategy

When this method returns, one alignment has been marked as primary according to the implementation's strategy.

Specified by:

pickPrimaryAlignment in interface PrimaryAlignmentSelectionStrategy