Package picard.sam
Class BestEndMapqPrimaryAlignmentStrategy
java.lang.Object
picard.sam.BestEndMapqPrimaryAlignmentStrategy
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PrimaryAlignmentSelectionStrategy
public class BestEndMapqPrimaryAlignmentStrategy
extends 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.
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
pickPrimaryAlignment
(picard.sam.HitsForInsert hits) Primary alignment was filtered out.
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Constructor Details
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BestEndMapqPrimaryAlignmentStrategy
public BestEndMapqPrimaryAlignmentStrategy()
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Method Details
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pickPrimaryAlignment
public void pickPrimaryAlignment(picard.sam.HitsForInsert hits) Primary alignment was filtered out. Need to select a new one.- Specified by:
pickPrimaryAlignment
in interfacePrimaryAlignmentSelectionStrategy
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