- All Implemented Interfaces:
- PrimaryAlignmentSelectionStrategy
public class BestMapqPrimaryAlignmentSelectionStrategy
extends java.lang.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.