Package org.broadinstitute.gatk.utils.smithwaterman

Examples of org.broadinstitute.gatk.utils.smithwaterman.SmithWaterman


        final Cigar nonStandard;

        final String paddedRef = SW_PAD + new String(refSeq) + SW_PAD;
        final String paddedPath = SW_PAD + new String(altSeq) + SW_PAD;
        final SmithWaterman alignment = new SWPairwiseAlignment( paddedRef.getBytes(), paddedPath.getBytes(), NEW_SW_PARAMETERS);

        if ( isSWFailure(alignment) ) {
            return null;
        }


        // cut off the padding bases
        final int baseStart = SW_PAD.length();
        final int baseEnd = paddedPath.length() - SW_PAD.length() - 1; // -1 because it's inclusive
        nonStandard = AlignmentUtils.trimCigarByBases(alignment.getCigar(), baseStart, baseEnd);

        if ( nonStandard.getReferenceLength() != refSeq.length ) {
            nonStandard.add(new CigarElement(refSeq.length - nonStandard.getReferenceLength(), CigarOperator.D));
        }
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