Package picard.sam
Class BestMapqPrimaryAlignmentSelectionStrategy
- java.lang.Object
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- picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
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- All Implemented Interfaces:
PrimaryAlignmentSelectionStrategy
public class BestMapqPrimaryAlignmentSelectionStrategy extends Object implements PrimaryAlignmentSelectionStrategy
This strategy was designed for TopHat output, but could be of general utility. It picks the alignment with best MAPQ. If paired-end, it is the alignment in which the sum of the MAPQs of both ends is the best. In case of ties, one is selected arbitrarily. This strategy expects pair-aware alignments, with the corresponding alignment for each mate of the pair correlated by HI (hit index) tag. If the aligner has set a pair of alignments as primary, this is used (assuming one of those alignments is not filtered out). Otherwise the alignment pair with best MapQ is selected.
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Constructor Summary
Constructors Constructor Description BestMapqPrimaryAlignmentSelectionStrategy()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
pickPrimaryAlignment(picard.sam.HitsForInsert hits)
Primary alignment was filtered out.
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Method Detail
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pickPrimaryAlignment
public void pickPrimaryAlignment(picard.sam.HitsForInsert hits)
Primary alignment was filtered out. Need to select a new one.- Specified by:
pickPrimaryAlignment
in interfacePrimaryAlignmentSelectionStrategy
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