Package net.sf.samtools

Examples of net.sf.samtools.Cigar

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//        System.out.println("o: " + origReadAltRef);
       
        if (origReadAltRef != null) {
          for (int i=indelPos; i>0; i--) {
            Cigar newCigar = shiftCigarLeft(read.getCigar(), i);
           
            String shiftedReadAltRef = c2r.getAlternateReference(read, newCigar);
           
            if ((shiftedReadAltRef != null) && (origReadAltRef.equals(shiftedReadAltRef))) {         
              SAMRecord newRead = cloneRead(read);
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      throw new RuntimeException(e);
    }
  }
 
  protected Cigar shiftCigarLeft(Cigar cigar, int positionsToShift) {
    Cigar newCigar = new Cigar();
   
    for (int i=0; i<cigar.getCigarElements().size(); i++) {
      CigarElement elem = cigar.getCigarElement(i);
     
      if (isFirstNonSoftClippedElem(i, cigar)) {
        int newLen = elem.getLength() - positionsToShift;
       
        if (newLen > 0) {
          CigarElement newElem = new CigarElement(newLen, elem.getOperator());
          newCigar.add(newElem);
        }
      } else if (isLastNonSoftClippedElem(i, cigar)) {
        if (elem.getOperator() == CigarOperator.M) {
          CigarElement newElem = new CigarElement(elem.getLength() + positionsToShift, CigarOperator.M);
          newCigar.add(newElem);
        } else {
          CigarElement newElem = new CigarElement(positionsToShift, CigarOperator.M);
          newCigar.add(elem);
          newCigar.add(newElem);
        }
      } else {
        newCigar.add(elem);
      }
    }
   
    return newCigar;
  }
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    Assert.assertEquals(read.getReadString(), "CCCCAGCC");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_exact() {
    Cigar cigar = getCigar("100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 0, 99);
    Assert.assertEquals(cigar2.toString(), "100M");
  }
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    Assert.assertEquals(cigar2.toString(), "100M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_lessThan1Elem() {
    Cigar cigar = getCigar("100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 0, 90);
    Assert.assertEquals(cigar2.toString(), "91M");
  }
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    Assert.assertEquals(cigar2.toString(), "91M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_lessThan1Elem2() {
    Cigar cigar = getCigar("100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 10, 99);
    Assert.assertEquals(cigar2.toString(), "90M");
  }
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    Assert.assertEquals(cigar2.toString(), "90M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_lessThan1Elem3() {
    Cigar cigar = getCigar("100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 10, 90);
    Assert.assertEquals(cigar2.toString(), "81M");
  }
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    Assert.assertEquals(cigar2.toString(), "81M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_lessThanFirstElem() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 10, 90);
    Assert.assertEquals(cigar2.toString(), "81M");
  }
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    Assert.assertEquals(cigar2.toString(), "81M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_spanElems1() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 0, 100);
    Assert.assertEquals(cigar2.toString(), "100M1I");
  }
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    Assert.assertEquals(cigar2.toString(), "100M1I");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_spanElems2() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 1, 100);
    Assert.assertEquals(cigar2.toString(), "99M1I");
  }
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    Assert.assertEquals(cigar2.toString(), "99M1I");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_spanElems3() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 1, 199);
    Assert.assertEquals(cigar2.toString(), "99M100I");
  }
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Related Classes of net.sf.samtools.Cigar

  • abra.cadabra.Cadabra
  • abra.cadabra.SimpleCaller
  • abra.CombineChimera3
  • abra.ContigChopper
  • abra.IndelShifter
  • abra.IndelShifterTest
  • abra.ReadBlock
  • abra.ReAligner
  • abra.SAMRecordUtils
  • abra.SAMRecordUtilsTest
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