Package htsjdk.samtools.SamPairUtil

Examples of htsjdk.samtools.SamPairUtil.PairOrientation

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                }
                else if (!sam.getMateReferenceIndex().equals(sam.getReferenceIndex())) {
                    crossChromPairs++;
                }
                else {
                    final PairOrientation pairOrientation = SamPairUtil.getPairOrientation(sam);
                    if (pairOrientation == PairOrientation.RF) {
                        outieHistogram.increment(absInsertSize);
                        outies++;
                        if (sam.getDuplicateReadFlag()) {
                            outieDupes++;
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Related Classes of htsjdk.samtools.SamPairUtil.PairOrientation

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