test/jalview/datamodel/CigarParserTest.java

   1 package jalview.datamodel;
   2
   3 import java.util.Iterator;
   4 import java.util.SortedMap;
   5 import java.util.TreeMap;
   6
   7 import org.testng.Assert;
   8 import org.testng.annotations.BeforeClass;
   9 import org.testng.annotations.DataProvider;
  10 import org.testng.annotations.Test;
  11
  12 import htsjdk.samtools.SAMRecord;
  13 import htsjdk.samtools.SAMRecordSetBuilder;
  14
  15 public class CigarParserTest
  16 {
  17   @BeforeClass(alwaysRun = true)
  18   public void setup()
  19   {
  20
  21
  22
  23   }
  24
  25   @DataProvider(name = "reads")
  26   public Object[][] createReadsData()
  27   {
  28     SortedMap<Integer, Integer> noinsertions = new TreeMap<>();
  29
  30     SortedMap<Integer, Integer> insertions = new TreeMap<>();
  31     insertions.put(8, 3);
  32     insertions.put(105, 2);
  33
  34     SortedMap<Integer, Integer> insertions2 = new TreeMap<>();
  35     insertions2.put(11, 2);
  36
  37     SortedMap<Integer, Integer> insertions3 = new TreeMap<>();
  38     insertions3.put(8, 3);
  39     insertions3.put(105, 3);
  40
  41     SortedMap<Integer, Integer> insertions4 = new TreeMap<>();
  42     insertions4.put(8, 3);
  43     insertions4.put(105, 2);
  44     insertions4.put(109, 3);
  45     insertions4.put(112, 1);
  46
  47     String read = "CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC";
  48
  49     return new Object[][] { { "1S84M2I14M", read, 21,
  50         "-----------------------GAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  51         insertions }, // first residue is G (accounting for C soft clip) at
  52                       // position 21 + 3 (insertions at position 8)
  53         { "1S84M2I14M", read, 21,
  54             "-----------------------GAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGA-GGAGCTCGTTGGTC",
  55             insertions3 }, // read has 2 insertions accounted for in
  56                            // insertions3, 3rd insertion is added as gap at
  57                            // position 105
  58         { "1S84M2I14M", read, 21,
  59             "-----------------------GAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAG---CTC-GTTGGTC",
  60             insertions4 }, // 2 insertions in read accounted for at position
  61                            // 105; 3 insertions at 109 and 1 insertion at 112
  62         { "44M1D57M",
  63         read,
  64         3,
  65             "--CGAAG---CTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTG-AAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  66         insertions },
  67         { "101M",
  68             read, 4,
  69             "---CGAA---GCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  70             insertions },
  71         { "6M2D76M19S",
  72             "CGAAGCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTCCC",
  73             4,
  74             "---CGAAGC----TTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGA",
  75             insertions2 },
  76
  77         { "44M1D57M",
  78             read,
  79             3,
  80             "--CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTG-AAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  81             noinsertions },
  82         { "101M",
  83             read, 4,
  84             "---CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  85             noinsertions },
  86         { "5S96M", read, 7,
  87             "------CTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  88             noinsertions },
  89         { "96M5H", read, 7,
  90             "------CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGT",
  91             noinsertions }, };
  92   }
  93
  94   @Test(dataProvider = "reads", groups = { "Functional" })
  95   public void testParse(String cigar, String read, int start, String result,
  96           SortedMap<Integer, Integer> insertions)
  97   {
  98     SAMRecord rec = new SAMRecord(null);
  99     rec.setCigarString(cigar);
 100     rec.setReadString(read);
 101     rec.setAlignmentStart(start);
 102
 103     CigarParser cp = new CigarParser('-');
 104     String bfresult = cp.parseCigarToSequence(rec, insertions, 1);
 105
 106     System.out.println(result);
 107     System.out.println(bfresult);
 108     Assert.assertEquals(bfresult, result);
 109   }
 110
 111   @Test(groups = { "Functional" })
 112   public void testGetInsertions()
 113   {
 114     final SAMRecordSetBuilder builder = new SAMRecordSetBuilder();
 115     builder.addFrag("read_1", 22, 30000, false, false,
 116             "101M", "", 0);
 117     builder.addFrag("read_2", 22, 28835, false, false,
 118             "50M3I48M", "", 0);
 119     builder.addFrag("read_3", 22, 28835, false, false, "3M1I75M2I1M", "",
 120             0);
 121     builder.addFrag("read_4", 22, 28865, false, false, "48M3I49M", "", 0);
 122     builder.addFrag("read_5", 22, 28865, false, false, "49M3I47M2D2M", "",
 123             0);
 124     builder.addFrag("read_6", 22, 27000, false, false, "2M4I90M5S", "", 0);
 125     builder.addFrag("read_7", 22, 27000, false, false, "2M1I98M", "", 0);
 126
 127     builder.addFrag("read_8", 22, 27000, false, false, "3M200N2I5M", "", 0);
 128
 129     Iterator<SAMRecord> it = builder.iterator();
 130     CigarParser cp = new CigarParser('-');
 131     SortedMap<Integer, Integer> insertions = cp.getInsertions(it);
 132     Assert.assertEquals(insertions.size(), 6);
 133     Assert.assertTrue(insertions.containsKey(28838));
 134     Assert.assertEquals((int) insertions.get(28838), 1);
 135     Assert.assertTrue(insertions.containsKey(28885));
 136     Assert.assertEquals((int) insertions.get(28885), 3);
 137     Assert.assertTrue(insertions.containsKey(28913));
 138     Assert.assertEquals((int) insertions.get(28913), 3);
 139     Assert.assertTrue(insertions.containsKey(28914));
 140     Assert.assertEquals((int) insertions.get(28914), 3);
 141     Assert.assertTrue(insertions.containsKey(27002));
 142     Assert.assertEquals((int) insertions.get(27002), 4);
 143     Assert.assertTrue(insertions.containsKey(27203));
 144     Assert.assertEquals((int) insertions.get(27203), 2);
 145   }
 146 }