Package picard.sam
Class EarliestFragmentPrimaryAlignmentSelectionStrategy
- java.lang.Object
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- picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
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- All Implemented Interfaces:
PrimaryAlignmentSelectionStrategy
public class EarliestFragmentPrimaryAlignmentSelectionStrategy extends 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.
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Constructor Summary
Constructors Constructor Description EarliestFragmentPrimaryAlignmentSelectionStrategy()
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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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