PrimaryAlignmentSelectionStrategy (picard 2.18.25 API)

All Known Implementing Classes:

BestEndMapqPrimaryAlignmentStrategy, BestMapqPrimaryAlignmentSelectionStrategy, EarliestFragmentPrimaryAlignmentSelectionStrategy, MostDistantPrimaryAlignmentSelectionStrategy
```
public interface PrimaryAlignmentSelectionStrategy
```
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate. Any pre-existing primary designation is ignored, so if the aligner has selected an appropriate primary alignment, this class should not be called.

Method Summary

All Methods Instance Methods Abstract 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.

- Method Detail
  - pickPrimaryAlignment
```
void pickPrimaryAlignment(picard.sam.HitsForInsert hitsForInsert)
```
    When this method returns, one alignment has been marked as primary according to the implementation's strategy.