Package net.sf.samtools

Examples of net.sf.samtools.Cigar

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    Assert.assertEquals(cigar2.toString(), "99M100I");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_skipElem() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 100, 199);
    Assert.assertEquals(cigar2.toString(), "100I");
  }
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    Assert.assertEquals(cigar2.toString(), "100I");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_skipElem2() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 200, 299);
    Assert.assertEquals(cigar2.toString(), "100M");
  }
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    Assert.assertEquals(cigar2.toString(), "100M");
  }

  @Test (groups = "unit")
  public void testSubsetCigar_skipAndSpan1() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 100, 249);
    Assert.assertEquals(cigar2.toString(), "100I50M");
  }
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    Assert.assertEquals(cigar2.toString(), "100I50M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_skipAndSpan2() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 150, 249);
    Assert.assertEquals(cigar2.toString(), "50I50M");
  }
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    Assert.assertEquals(cigar2.toString(), "50I50M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_spanAll1() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 0, 299);
    Assert.assertEquals(cigar2.toString(), "100M100I100M");
  }
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    Assert.assertEquals(cigar2.toString(), "100M100I100M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_spanAll2() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 0, 298);
    Assert.assertEquals(cigar2.toString(), "100M100I99M");
  }
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    Assert.assertEquals(cigar2.toString(), "100M100I99M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_spanAll3() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 1, 299);
    Assert.assertEquals(cigar2.toString(), "99M100I100M");
  }
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    Assert.assertEquals(cigar2.toString(), "99M100I100M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_spanAll4() {
    Cigar cigar = getCigar("100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 1, 298);
    Assert.assertEquals(cigar2.toString(), "99M100I99M");
  }
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    Assert.assertEquals(cigar2.toString(), "99M100I99M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_long() {
    Cigar cigar = getCigar("100M100I100M100I100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 1, 498);
    Assert.assertEquals(cigar2.toString(), "99M100I100M100I99M");
  }
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    Assert.assertEquals(cigar2.toString(), "99M100I100M100I99M");
  }
 
  @Test (groups = "unit")
  public void testSubsetCigar_deletion() {
    Cigar cigar = getCigar("100M100D100M");
    Cigar cigar2 = SAMRecordUtils.subset(cigar, 1, 198);
    Assert.assertEquals(cigar2.toString(), "99M100D99M");
  }
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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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