picard.sam

Class EarliestFragmentPrimaryAlignmentSelectionStrategy

java.lang.Object

picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy

All Implemented Interfaces:

PrimaryAlignmentSelectionStrategy

public class EarliestFragmentPrimaryAlignmentSelectionStrategy
extends java.lang.Object
implements PrimaryAlignmentSelectionStrategy

When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps the earliest base in the read. This implementation only works for fragments, not for pairs. If there are multiple alignments that all start mapping at the same offest in the read, pick the one with the best MAPQ. If there are multiple alignments that have the earliest mapping and that have the same MAPQ, pick one randomly.

Constructor Summary

Constructors

Constructor and Description
EarliestFragmentPrimaryAlignmentSelectionStrategy()

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

EarliestFragmentPrimaryAlignmentSelectionStrategy

public EarliestFragmentPrimaryAlignmentSelectionStrategy()

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