Package htsjdk.samtools

Examples of htsjdk.samtools.Cigar

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        filter = new NDNCigarReadTransformer();
    }

    @Test(dataProvider = "filteringIteratorTestData")
    public void testCigarRefactoring (final String originalCigarString, final String expectedString) {
        Cigar originalCigar = CigarUtils.cigarFromString(originalCigarString);
        String actualString = filter.refactorNDNtoN(originalCigar).toString();
        Assert.assertEquals(actualString, expectedString, "ciagr string "+ originalCigarString+" should become: "+expectedString+" but got: "+actualString);
    }
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        Assert.assertFalse(filter.filterOut(nonNContainingCigarRead));
    }

    protected SAMRecord buildSAMRecord(final String cigarString) {
        final Cigar nContainingCigar = TextCigarCodec.getSingleton().decode(cigarString);
        return  this.createRead(nContainingCigar, 1, 0, 10);
    }
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*/

public class BadCigarFilter extends ReadFilter {

    public boolean filterOut(final SAMRecord rec) {
        final Cigar c = rec.getCigar();

        // if there is no Cigar then it can't be bad
        if( c.isEmpty() ) {
            return false;
        }

        Iterator<CigarElement> elementIterator = c.getCigarElements().iterator();

        CigarOperator firstOp = CigarOperator.H;
        while (elementIterator.hasNext() && (firstOp == CigarOperator.H || firstOp == CigarOperator.S)) {
            CigarOperator op = elementIterator.next().getOperator();

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    @Override
    public GATKSAMRecord apply(final GATKSAMRecord read) {
        if(read == null)
            throw new UserException.BadInput("try to transform a null GATKSAMRecord");
        final Cigar originalCigar = read.getCigar();
        if (originalCigar.isValid(read.getReadName(),-1) != null)
            throw new UserException.BadInput("try to transform a read with non-valid cigar string: readName: "+read.getReadName()+" Cigar String: "+originalCigar);
        read.setCigar(refactorNDNtoN(originalCigar));
        return read;
    }
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    }



    protected Cigar refactorNDNtoN(final Cigar originalCigar) {
        final Cigar refactoredCigar = new Cigar();
        final int cigarLength = originalCigar.numCigarElements();
        for(int i = 0; i < cigarLength; i++){
            final CigarElement element = originalCigar.getCigarElement(i);
            if(element.getOperator() == CigarOperator.N && thereAreAtLeast2MoreElements(i,cigarLength)){
                final CigarElement nextElement = originalCigar.getCigarElement(i+1);
                final CigarElement nextNextElement = originalCigar.getCigarElement(i+2);

                // if it is N-D-N replace with N (with the total length) otherwise just add the first N.
                if(nextElement.getOperator() == CigarOperator.D && nextNextElement.getOperator() == CigarOperator.N){
                    final int threeElementsLength = element.getLength() + nextElement.getLength() + nextNextElement.getLength();
                    final CigarElement refactoredElement = new CigarElement(threeElementsLength,CigarOperator.N);
                    refactoredCigar.add(refactoredElement);
                    i += 2; //skip the elements that were refactored
                }
                else
                    refactoredCigar.add(element);  // add only the first N
            }
            else
                refactoredCigar.add(element);  // add any non-N element
        }
        return refactoredCigar;
    }
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        byte [] cigarCombination = new byte[maximumLength];

        Utils.fillArrayWithByte(cigarCombination, (byte) 0);               // we start off with all 0's in the combination array.
        int currentIndex = 0;
        while (true) {
            Cigar cigar = createCigarFromCombination(cigarCombination, cigarElements);    // create the cigar
            cigar = CigarUtils.combineAdjacentCigarElements(cigar);                   // combine adjacent elements
            if (CigarUtils.isCigarValid(cigar)) {                                     // check if it's valid
                cigarList.add(cigar);                                      // add it
            }
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        return cigarList;
    }

    private static Cigar createCigarFromCombination(byte[] cigarCombination, CigarElement[] cigarElements) {
        Cigar cigar = new Cigar();
        for (byte i : cigarCombination) {
            cigar.add(cigarElements[i]);
        }
        return cigar;
    }
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    public void testSimpleInsertionAllele() {
        final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";

        final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
        h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
        final Cigar h1Cigar = new Cigar(h1CigarList);
        String h1bases = "AACTTCTGGTCAACTGGTCAACTGGTCAACTGGTCA";
        basicInsertTest("A", "AACTT", 0, h1Cigar, bases, h1bases);
        h1bases = "ACTGGTCAACTTACTGGTCAACTGGTCAACTGGTCA";
        basicInsertTest("A", "AACTT", 7, h1Cigar, bases, h1bases);
        h1bases = "ACTGGTCAACTGGTCAAACTTCTGGTCAACTGGTCA";
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    public void testSimpleDeletionAllele() {
        final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";

        final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
        h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
        final Cigar h1Cigar = new Cigar(h1CigarList);
        String h1bases = "ATCAACTGGTCAACTGGTCAACTGGTCA";
        basicInsertTest("ACTGG", "A", 0, h1Cigar, bases, h1bases);
        h1bases = "ACTGGTCAGTCAACTGGTCAACTGGTCA";
        basicInsertTest("AACTG", "A", 7, h1Cigar, bases, h1bases);
        h1bases = "ACTGGTCAACTGGTCAATCAACTGGTCA";
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    public void testSimpleSNPAllele() {
        final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";

        final ArrayList<CigarElement> h1CigarList = new ArrayList<CigarElement>();
        h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
        final Cigar h1Cigar = new Cigar(h1CigarList);
        String h1bases = "AGTGGTCAACTGGTCAACTGGTCAACTGGTCA";
        basicInsertTest("C", "G", 1, h1Cigar, bases, h1bases);
        h1bases = "ACTGGTCTACTGGTCAACTGGTCAACTGGTCA";
        basicInsertTest("A", "T", 7, h1Cigar, bases, h1bases);
        h1bases = "ACTGGTCAACTGGTCAAATGGTCAACTGGTCA";
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Related Classes of htsjdk.samtools.Cigar

  • bcbio.gatk.tools.walkers.LeftAlignVariants
  • bcbio.variation.annotate.ReadMeanLen
  • bcbio.variation.annotate.ReadMeanPos
  • bcbio.variation.annotate.ReadPosEndDist
  • org.broad.igv.ga4gh.Ga4ghAlignment
  • org.broad.igv.sam.reader.SamUtils
  • org.broadinstitute.gatk.engine.alignment.bwa.java.AlignmentMatchSequence
  • org.broadinstitute.gatk.engine.datasources.reads.TheoreticalMinimaBenchmark
  • org.broadinstitute.gatk.engine.filters.BadCigarFilter
  • org.broadinstitute.gatk.engine.filters.MalformedReadFilterUnitTest
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