Package net.sf.samtools

Examples of net.sf.samtools.Cigar

13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
 
  private IndelShifter indelShifter = new IndelShifter();

  @Test (groups = "unit" )
  public void testShiftCigarLeft_basic() {
    Cigar cigar = new Cigar();
   
    cigar.add(new CigarElement(10, CigarOperator.M));
    cigar.add(new CigarElement(3, CigarOperator.D));
    cigar.add(new CigarElement(40, CigarOperator.M));
   
    Cigar newCigar;

    newCigar = indelShifter.shiftCigarLeft(cigar, 10);
    Assert.assertEquals(newCigar.toString(), "3D50M");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 9);
    Assert.assertEquals(newCigar.toString(), "1M3D49M");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 8);
    Assert.assertEquals(newCigar.toString(), "2M3D48M");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 4);
    Assert.assertEquals(newCigar.toString(), "6M3D44M");

    newCigar = indelShifter.shiftCigarLeft(cigar, 2);
    Assert.assertEquals(newCigar.toString(), "8M3D42M");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 1);
    Assert.assertEquals(newCigar.toString(), "9M3D41M");
  }
View Full Code Here
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
    Assert.assertEquals(newCigar.toString(), "9M3D41M");
  }
 
  @Test (groups = "unit" )
  public void testShiftCigarLeft_softClipping() {
    Cigar cigar = new Cigar();
   
    cigar.add(new CigarElement(2, CigarOperator.S));
    cigar.add(new CigarElement(6, CigarOperator.M));
    cigar.add(new CigarElement(2, CigarOperator.I));
    cigar.add(new CigarElement(30, CigarOperator.M));
    cigar.add(new CigarElement(10, CigarOperator.S));
   
    Cigar newCigar;

    newCigar = indelShifter.shiftCigarLeft(cigar, 6);
    Assert.assertEquals(newCigar.toString(), "2S2I36M10S");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 5);
    Assert.assertEquals(newCigar.toString(), "2S1M2I35M10S");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 4);
    Assert.assertEquals(newCigar.toString(), "2S2M2I34M10S");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 3);
    Assert.assertEquals(newCigar.toString(), "2S3M2I33M10S");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 2);
    Assert.assertEquals(newCigar.toString(), "2S4M2I32M10S");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 1);
    Assert.assertEquals(newCigar.toString(), "2S5M2I31M10S");
  }
View Full Code Here
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
    Assert.assertEquals(newCigar.toString(), "2S5M2I31M10S");
  }
 
  @Test (groups = "unit" )
  public void testShiftCigarLeft_insertAtTail() {
    Cigar cigar = new Cigar();
   
    cigar.add(new CigarElement(40, CigarOperator.M));
    cigar.add(new CigarElement(10, CigarOperator.I));
   
    Cigar newCigar;

    newCigar = indelShifter.shiftCigarLeft(cigar, 40);
    Assert.assertEquals(newCigar.toString(), "10I40M");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 39);
    Assert.assertEquals(newCigar.toString(), "1M10I39M");

    newCigar = indelShifter.shiftCigarLeft(cigar, 30);
    Assert.assertEquals(newCigar.toString(), "10M10I30M");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 1);
    Assert.assertEquals(newCigar.toString(), "39M10I1M");
  }
View Full Code Here
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
    Assert.assertEquals(newCigar.toString(), "39M10I1M");
  }
 
  @Test (groups = "unit" )
  public void testShiftCigarLeft_multipleIndels() {
    Cigar cigar = new Cigar();
   
    cigar.add(new CigarElement(20, CigarOperator.M));
    cigar.add(new CigarElement(1, CigarOperator.I));
    cigar.add(new CigarElement(5, CigarOperator.M));
    cigar.add(new CigarElement(3, CigarOperator.D));
    cigar.add(new CigarElement(24, CigarOperator.M));
   
    Cigar newCigar;
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 20);
    Assert.assertEquals(newCigar.toString(), "1I5M3D44M");
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 10);
    Assert.assertEquals(newCigar.toString(), "10M1I5M3D34M");

    newCigar = indelShifter.shiftCigarLeft(cigar, 1);
    Assert.assertEquals(newCigar.toString(), "19M1I5M3D25M");
  }
View Full Code Here
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
  }
 
  @Test (groups = "unit" )
  public void testShiftCigarLeft_complex() {
    //3S69M1I18M1D9M
    Cigar cigar = new Cigar();
   
    cigar.add(new CigarElement(3, CigarOperator.S));
    cigar.add(new CigarElement(69, CigarOperator.M));
    cigar.add(new CigarElement(1, CigarOperator.I));
    cigar.add(new CigarElement(18, CigarOperator.M));
    cigar.add(new CigarElement(1, CigarOperator.D));
    cigar.add(new CigarElement(9, CigarOperator.M));
   
    Cigar newCigar;
   
    newCigar = indelShifter.shiftCigarLeft(cigar, 1);
    Assert.assertEquals(newCigar.toString(), "3S68M1I18M1D10M");
  }
View Full Code Here
143
144
145
146
147
148
149
    record.setReadBases(newBases);

    byte[] newScores = new byte[newLength];
    System.arraycopy(record.getBaseQualities(), 0, newScores, 0, newLength);

    record.setCigar(new Cigar(newCigarElements));
  }
View Full Code Here
406
407
408
409
410
411
412
413
414
415
416
417
  public static void calculateMdAndNmTags(SAMRecord record, byte[] ref,
      boolean calcMD, boolean calcNM) {
    if (!calcMD && !calcNM)
      return;

    Cigar cigar = record.getCigar();
    List<CigarElement> cigarElements = cigar.getCigarElements();
    byte[] seq = record.getReadBases();
    int start = record.getAlignmentStart() - 1;
    int i, x, y, u = 0;
    int nm = 0;
    StringBuffer str = new StringBuffer();
View Full Code Here
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
  private static final Cigar getCigar2(Collection<ReadFeature> features,
      int readLength) {
    if (features == null || features.isEmpty()) {
      CigarElement ce = new CigarElement(readLength, CigarOperator.M);
      return new Cigar(Arrays.asList(ce));
    }

    List<CigarElement> list = new ArrayList<CigarElement>();
    int totalOpLen = 1;
    CigarElement ce;
    CigarOperator lastOperator = CigarOperator.MATCH_OR_MISMATCH;
    int lastOpLen = 0;
    int lastOpPos = 1;
    CigarOperator co = null;
    int rfLen = 0;
    for (ReadFeature f : features) {

      int gap = f.getPosition() - (lastOpPos + lastOpLen);
      if (gap > 0) {
        if (lastOperator != CigarOperator.MATCH_OR_MISMATCH) {
          list.add(new CigarElement(lastOpLen, lastOperator));
          lastOpPos += lastOpLen;
          totalOpLen += lastOpLen;
          lastOpLen = gap;
        } else {
          lastOpLen += gap;
        }

        lastOperator = CigarOperator.MATCH_OR_MISMATCH;
      }

      switch (f.getOperator()) {
      case Insertion.operator:
        co = CigarOperator.INSERTION;
        rfLen = ((Insertion) f).getSequence().length;
        break;
      case SoftClip.operator:
        co = CigarOperator.SOFT_CLIP;
        rfLen = ((SoftClip) f).getSequence().length;
        break;
      case HardClip.operator:
        co = CigarOperator.HARD_CLIP ;
        rfLen = ((HardClip) f).getSequence().length;
        break;
      case InsertBase.operator:
        co = CigarOperator.INSERTION;
        rfLen = 1;
        break;
      case Deletion.operator:
        co = CigarOperator.DELETION;
        rfLen = ((Deletion) f).getLength();
        break;
      case RefSkip.operator:
        co = CigarOperator.SKIPPED_REGION;
        rfLen = ((RefSkip) f).getLength();
        break;
      case Padding.operator:
        co = CigarOperator.PADDING ;
        rfLen = ((Padding) f).getLength();
        break;
      case Substitution.operator:
      case ReadBase.operator:
        co = CigarOperator.MATCH_OR_MISMATCH;
        rfLen = 1;
        break;
      default:
        continue;
      }

      if (lastOperator != co) {
        // add last feature
        if (lastOpLen > 0) {
          list.add(new CigarElement(lastOpLen, lastOperator));
          totalOpLen += lastOpLen;
        }
        lastOperator = co;
        lastOpLen = rfLen;
        lastOpPos = f.getPosition();
      } else
        lastOpLen += rfLen;

      if (!co.consumesReadBases())
        lastOpPos -= rfLen;
    }

    if (lastOperator != null) {
      if (lastOperator != CigarOperator.M) {
        list.add(new CigarElement(lastOpLen, lastOperator));
        if (readLength >= lastOpPos + lastOpLen) {
          ce = new CigarElement(readLength - (lastOpLen + lastOpPos)
              + 1, CigarOperator.M);
          list.add(ce);
        }
      } else if (readLength > lastOpPos - 1) {
        ce = new CigarElement(readLength - lastOpPos + 1,
            CigarOperator.M);
        list.add(ce);
      }
    }

    if (list.isEmpty()) {
      ce = new CigarElement(readLength, CigarOperator.M);
      return new Cigar(Arrays.asList(ce));
    }

    return new Cigar(list);
  }
View Full Code Here
TOP

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
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.