Package picard.sam.HitsForInsert

Examples of picard.sam.HitsForInsert.NumPrimaryAlignmentState


    public void pickPrimaryAlignment(final HitsForInsert hits) {

        if (hits.numHits() == 0) throw new IllegalArgumentException("No alignments to pick from");
        hits.coordinateByHitIndex();
        // See if primary alignment is not already unambiguously determined.
        final NumPrimaryAlignmentState firstEndAlignmentState = hits.tallyPrimaryAlignments(true);
        final NumPrimaryAlignmentState secondEndAlignmentState = hits.tallyPrimaryAlignments(false);

        if ((firstEndAlignmentState == NumPrimaryAlignmentState.NONE && secondEndAlignmentState == NumPrimaryAlignmentState.NONE) ||
                firstEndAlignmentState == NumPrimaryAlignmentState.MORE_THAN_ONE ||
                secondEndAlignmentState == NumPrimaryAlignmentState.MORE_THAN_ONE) {
            // Need to use selected strategy for picking primary.
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Related Classes of picard.sam.HitsForInsert.NumPrimaryAlignmentState

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