Package picard.sam
Class MostDistantPrimaryAlignmentSelectionStrategy
- java.lang.Object
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- picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
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- All Implemented Interfaces:
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 Constructor Description MostDistantPrimaryAlignmentSelectionStrategy()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
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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Method Detail
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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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