Examples of CigarElement

Examples of htsjdk.samtools.CigarElement


        // Construct the test path
        Path<SeqVertex,BaseEdge> path = Path.makePath(Arrays.asList(top, alt, bot), graph);


        Cigar expected = new Cigar();
        expected.add(new CigarElement(padSize, CigarOperator.M));
        if ( ! prefix.equals("") ) expected.add(new CigarElement(prefix.length(), CigarOperator.M));
        for ( final CigarElement elt : TextCigarCodec.getSingleton().decode(midCigar).getCigarElements() ) expected.add(elt);
        if ( ! end.equals("") ) expected.add(new CigarElement(end.length(), CigarOperator.M));
        expected.add(new CigarElement(padSize, CigarOperator.M));
        expected = AlignmentUtils.consolidateCigar(expected);


        final String refString = top.getSequenceString() + ref.getSequenceString() + bot.getSequenceString();
        final Cigar pathCigar = path.calculateCigar(refString.getBytes());

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Examples of htsjdk.samtools.CigarElement

            for ( final int indelOp1 : Arrays.asList(1, -1) ) {
                for ( final int indelSize2 : Arrays.asList(1, 2, 3, 4) ) {
                    for ( final int indelOp2 : Arrays.asList(1, -1) ) {


                        Cigar expectedCigar = new Cigar();
                        expectedCigar.add(new CigarElement(refString.length(), CigarOperator.M));
                        expectedCigar.add(new CigarElement(indelSize1, (indelOp1 > 0 ? CigarOperator.I : CigarOperator.D)));
                        expectedCigar.add(new CigarElement((indelOp1 < 0 ? refIndel1 - indelSize1 : refIndel1), CigarOperator.M));
                        expectedCigar.add(new CigarElement(refString.length(), CigarOperator.M));
                        expectedCigar.add(new CigarElement(indelSize2 * 2, (indelOp2 > 0 ? CigarOperator.I : CigarOperator.D)));
                        expectedCigar.add(new CigarElement((indelOp2 < 0 ? (refIndel2 - indelSize2) * 2 : refIndel2 * 2), CigarOperator.M));
                        expectedCigar.add(new CigarElement(refString.length(), CigarOperator.M));


                        Cigar givenCigar = new Cigar();
                        givenCigar.add(new CigarElement(refString.length() + refIndel1/2, CigarOperator.M));
                        givenCigar.add(new CigarElement(indelSize1, (indelOp1 > 0 ? CigarOperator.I : CigarOperator.D)));
                        givenCigar.add(new CigarElement((indelOp1 < 0 ? (refIndel1/2 - indelSize1) : refIndel1/2) + refString.length() + refIndel2/2 * 2, CigarOperator.M));
                        givenCigar.add(new CigarElement(indelSize2 * 2, (indelOp2 > 0 ? CigarOperator.I : CigarOperator.D)));
                        givenCigar.add(new CigarElement((indelOp2 < 0 ? (refIndel2/2 - indelSize2) * 2 : refIndel2/2 * 2) + refString.length(), CigarOperator.M));


                        String theRef = preRefString + refString + Utils.dupString(indelString1, refIndel1) + refString + Utils.dupString(indelString2, refIndel2) + refString + postRefString;
                        String theRead = refString + Utils.dupString(indelString1, refIndel1 + indelOp1 * indelSize1) + refString + Utils.dupString(indelString2, refIndel2 + indelOp2 * indelSize2) + refString;


                        Cigar calculatedCigar = CigarUtils.leftAlignCigarSequentially(AlignmentUtils.consolidateCigar(givenCigar), theRef.getBytes(), theRead.getBytes(), preRefString.length(), 0);

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Examples of htsjdk.samtools.CigarElement


    private int getNumClippedBasesAtStart(final SAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        final CigarElement first = c.getCigarElement(0);


        int numStartClippedBases = 0;
        if (first.getOperator() == CigarOperator.H) {
            numStartClippedBases = first.getLength();
        }
        final byte[] unclippedReadBases = read.getReadBases();
        final byte[] unclippedReadQuals = read.getBaseQualities();


        // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative,

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Examples of htsjdk.samtools.CigarElement


    private int getNumClippedBasesAtEnd(final GATKSAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        CigarElement last = c.getCigarElement(c.numCigarElements() - 1);


        int numEndClippedBases = 0;
        if (last.getOperator() == CigarOperator.H) {
            numEndClippedBases = last.getLength();
        }
        final byte[] unclippedReadBases = read.getReadBases();
        final byte[] unclippedReadQuals = read.getBaseQualities();


        // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative,

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Examples of htsjdk.samtools.CigarElement

                    break;
                case MATCH:
                case TRANSITION:
                case COMPLEMENT:
                case TRANSVERSION:
                    cigarElements.add(new CigarElement(size, CigarOperator.M));
                    break;
                case INSERTION:
                    cigarElements.add(new CigarElement(size,CigarOperator.I));
                    break;
                case DELETION:
                    cigarElements.add(new CigarElement(size,CigarOperator.D));
                    break;
                default:
            }
       }


       // No we look for consequitive elements with the same operator and we merge them.
       final ListIterator<CigarElement> it = cigarElements.listIterator();
       while (it.hasNext()) {
            final CigarElement thisElement = it.next();
            if (!it.hasNext())
                continue;
            final CigarElement nextElement = it.next();
            if (thisElement.getOperator() == nextElement.getOperator()) {
                final int nextLength = nextElement.getLength();
                it.remove();
                it.previous();
                it.set(new CigarElement(thisElement.getLength() + nextLength, thisElement.getOperator()));
            } else
                it.previous();
       }
       return new Cigar(cigarElements);
    }

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Examples of htsjdk.samtools.CigarElement




    private List<Haplotype> assemble(final ReadThreadingAssembler assembler, final byte[] refBases, final GenomeLoc loc, final List<GATKSAMRecord> reads) {
        final Haplotype refHaplotype = new Haplotype(refBases, true);
        final Cigar c = new Cigar();
        c.add(new CigarElement(refHaplotype.getBases().length, CigarOperator.M));
        refHaplotype.setCigar(c);


        final ActiveRegion activeRegion = new ActiveRegion(loc, null, true, genomeLocParser, 0);
        activeRegion.addAll(reads);
//        logger.warn("Assembling " + activeRegion + " with " + engine);

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Examples of htsjdk.samtools.CigarElement

     * @return 1 if merge was successful, 0 otherwise
     */
    protected int mergeDanglingTail(final DanglingChainMergeHelper danglingTailMergeResult) {


        final List<CigarElement> elements = danglingTailMergeResult.cigar.getCigarElements();
        final CigarElement lastElement = elements.get(elements.size() - 1);
        if ( lastElement.getOperator() != CigarOperator.M )
            throw new IllegalArgumentException("The last Cigar element must be an M");


        final int lastRefIndex = danglingTailMergeResult.cigar.getReferenceLength() - 1;
        final int matchingSuffix = Math.min(GraphUtils.longestSuffixMatch(danglingTailMergeResult.referencePathString, danglingTailMergeResult.danglingPathString, lastRefIndex), lastElement.getLength());
        if ( matchingSuffix == 0 )
            return 0;


        final int altIndexToMerge = Math.max(danglingTailMergeResult.cigar.getReadLength() - matchingSuffix - 1, 0);

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Examples of htsjdk.samtools.CigarElement

     * @return 1 if merge was successful, 0 otherwise
     */
    protected int mergeDanglingHead(final DanglingChainMergeHelper danglingHeadMergeResult) {


        final List<CigarElement> elements = danglingHeadMergeResult.cigar.getCigarElements();
        final CigarElement firstElement = elements.get(0);
        if ( firstElement.getOperator() != CigarOperator.M )
            throw new IllegalArgumentException("The first Cigar element must be an M");


        final int indexesToMerge = bestPrefixMatch(danglingHeadMergeResult.referencePathString, danglingHeadMergeResult.danglingPathString, firstElement.getLength());
        if ( indexesToMerge <= 0 )
            return 0;


        // we can't push back the reference path
        if ( indexesToMerge >= danglingHeadMergeResult.referencePath.size() - 1 )

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Examples of htsjdk.samtools.CigarElement

        List<CigarElement> paddedC=rawPadded.getCigarElements();
        List<CigarElement> notPaddedC=notPadded.getCigarElements();
        Assert.assertEquals(paddedC.size(),notPaddedC.size());
        for(int i=0;i<notPaddedC.size();i++)
        {
            CigarElement pc=paddedC.get(i);
            CigarElement npc=notPaddedC.get(i);
            if(pc.getOperator()== CigarOperator.M && npc.getOperator()==CigarOperator.M)
            {
                continue;
            }
            int l1=pc.getLength();
            int l2=npc.getLength();
            Assert.assertEquals(l1,l2);
            Assert.assertEquals(pc.getOperator(),npc.getOperator());
        }
    }

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Examples of htsjdk.samtools.CigarElement

                }
                cigarElementStack.push(cigarElement);
            }


            while (!cigarElementStack.empty()) {
                CigarElement cigarElement = cigarElementStack.pop();
                if (cigarElement.getOperator() != CigarOperator.SOFT_CLIP && cigarElement.getOperator() != CigarOperator.HARD_CLIP) {
                    endingOp = cigarElement.getOperator();
                    break;
                }
            }


            if (startingOp != CigarOperator.DELETION && endingOp != CigarOperator.DELETION && startingOp != CigarOperator.SKIPPED_REGION && endingOp != CigarOperator.SKIPPED_REGION)

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