Package picard.sam
Class BestEndMapqPrimaryAlignmentStrategy
- java.lang.Object
-
- picard.sam.BestEndMapqPrimaryAlignmentStrategy
-
- All Implemented Interfaces:
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.
-
-
Constructor Summary
Constructors Constructor Description BestEndMapqPrimaryAlignmentStrategy()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
pickPrimaryAlignment(picard.sam.HitsForInsert hits)
Primary alignment was filtered out.
-
-
-
Method Detail
-
pickPrimaryAlignment
public void pickPrimaryAlignment(picard.sam.HitsForInsert hits)
Primary alignment was filtered out. Need to select a new one.- Specified by:
pickPrimaryAlignment
in interfacePrimaryAlignmentSelectionStrategy
-
-