Package picard.sam
Class MostDistantPrimaryAlignmentSelectionStrategy
java.lang.Object
picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
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PrimaryAlignmentSelectionStrategy
public class MostDistantPrimaryAlignmentSelectionStrategy
extends 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.
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
pickPrimaryAlignment
(picard.sam.HitsForInsert hitsForInsert) When this method returns, one alignment has been marked as primary according to the implementation's strategy.
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Constructor Details
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MostDistantPrimaryAlignmentSelectionStrategy
public MostDistantPrimaryAlignmentSelectionStrategy()
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Method Details
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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 interfacePrimaryAlignmentSelectionStrategy
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