Package picard.sam

Class BestMapqPrimaryAlignmentSelectionStrategy

java.lang.Object

picard.sam.BestMapqPrimaryAlignmentSelectionStrategy

All Implemented Interfaces:

PrimaryAlignmentSelectionStrategy

public class BestMapqPrimaryAlignmentSelectionStrategy
extends Object
implements PrimaryAlignmentSelectionStrategy

This strategy was designed for TopHat output, but could be of general utility. It picks the alignment with best MAPQ. If paired-end, it is the alignment in which the sum of the MAPQs of both ends is the best. In case of ties, one is selected arbitrarily. This strategy expects pair-aware alignments, with the corresponding alignment for each mate of the pair correlated by HI (hit index) tag. If the aligner has set a pair of alignments as primary, this is used (assuming one of those alignments is not filtered out). Otherwise the alignment pair with best MapQ is selected.

Constructor Summary

Constructors

Constructor	Description
BestMapqPrimaryAlignmentSelectionStrategy()

Method Summary

Modifier and Type	Method	Description
void	pickPrimaryAlignment(picard.sam.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 Details

BestMapqPrimaryAlignmentSelectionStrategy

public BestMapqPrimaryAlignmentSelectionStrategy()

Method Details

pickPrimaryAlignment

public void pickPrimaryAlignment(picard.sam.HitsForInsert hits)

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

Specified by:

pickPrimaryAlignment in interface PrimaryAlignmentSelectionStrategy