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     String read = "CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC";
  42
  43     return new Object[][] { { "1S84M2I14M", read, 21,
  44         "-----------------------GAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  45         insertions },
  46         { "1S84M2I14M", read, 21,
  47             "-----------------------GAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGA-GGAGCTCGTTGGTC",
  48             insertions3 },
  49
  50         { "44M1D57M",
  51         read,
  52         3,
  53             "--CGAAG---CTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTG-AAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  54         insertions },
  55         { "101M",
  56             read, 4,
  57             "---CGAA---GCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  58             insertions },
  59         { "6M2D76M19S",
  60             "CGAAGCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTCCC",
  61             4,
  62             "---CGAAGC----TTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGA",
  63             insertions2 },
  64
  65         { "44M1D57M",
  66             read,
  67             3,
  68             "--CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTG-AAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  69             noinsertions },
  70         { "101M",
  71             read, 4,
  72             "---CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  73             noinsertions },
  74         { "5S96M", read, 7,
  75             "------CTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
  76             noinsertions },
  77         { "96M5H", read, 7,
  78             "------CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGT",
  79             noinsertions }, };
  80   }
  81
  82   @Test(dataProvider = "reads", groups = { "Functional" })
  83   public void testParse(String cigar, String read, int start, String result,
  84           SortedMap<Integer, Integer> insertions)
  85   {
  86     SAMRecord rec = new SAMRecord(null);
  87     rec.setCigarString(cigar);
  88     rec.setReadString(read);
  89     rec.setAlignmentStart(start);
  90
  91     CigarParser cp = new CigarParser('-');
  92     String bfresult = cp.parseCigarToSequence(rec, insertions);
  93
  94     System.out.println(result);
  95     System.out.println(bfresult);
  96     Assert.assertEquals(bfresult, result);
  97   }
  98
  99   @Test(groups = { "Functional" })
 100   public void testGetInsertions()
 101   {
 102     final SAMRecordSetBuilder builder = new SAMRecordSetBuilder();
 103     builder.addFrag("read_1", 22, 30000, false, false,
 104             "101M", "", 0);
 105     builder.addFrag("read_2", 22, 28835, false, false,
 106             "50M3I48M", "", 0);
 107     builder.addFrag("read_3", 22, 28835, false, false, "3M1I75M2I1M", "",
 108             0);
 109     builder.addFrag("read_4", 22, 28865, false, false, "48M3I49M", "", 0);
 110     builder.addFrag("read_5", 22, 28865, false, false, "49M3I47M2D2M", "",
 111             0);
 112     builder.addFrag("read_6", 22, 27000, false, false, "2M4I90M5S", "", 0);
 113     builder.addFrag("read_7", 22, 27000, false, false, "2M1I98M", "", 0);
 114
 115     Iterator<SAMRecord> it = builder.iterator();
 116     CigarParser cp = new CigarParser('-');
 117     SortedMap<Integer, Integer> insertions = cp.getInsertions(it);
 118     Assert.assertEquals(insertions.size(), 5);
 119     Assert.assertTrue(insertions.containsKey(28838));
 120     Assert.assertEquals((int) insertions.get(28838), 1);
 121     Assert.assertTrue(insertions.containsKey(28885));
 122     Assert.assertEquals((int) insertions.get(28885), 3);
 123     Assert.assertTrue(insertions.containsKey(28913));
 124     Assert.assertEquals((int) insertions.get(28913), 3);
 125     Assert.assertTrue(insertions.containsKey(28914));
 126     Assert.assertEquals((int) insertions.get(28914), 3);
 127     Assert.assertTrue(insertions.containsKey(27002));
 128     Assert.assertEquals((int) insertions.get(27002), 4);
 129   }
 130 }