JAL-2909 Updated tests

[jalview.git] / test / jalview / datamodel / CigarParserTest.java

diff --git a/test/jalview/datamodel/CigarParserTest.java b/test/jalview/datamodel/CigarParserTest.java
index 84a432e..80121ee 100644 (file)
--- a/test/jalview/datamodel/CigarParserTest.java
+++ b/test/jalview/datamodel/CigarParserTest.java
@@ -38,15 +38,27 @@ public class CigarParserTest
     insertions3.put(8, 3);
     insertions3.put(105, 3);
 
+    SortedMap<Integer, Integer> insertions4 = new TreeMap<>();
+    insertions4.put(8, 3);
+    insertions4.put(105, 2);
+    insertions4.put(109, 3);
+    insertions4.put(112, 1);
+
     String read = "CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC";
 
     return new Object[][] { { "1S84M2I14M", read, 21,
-        "----------------------cGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
-        insertions },
+        "-----------------------GAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
+        insertions }, // first residue is G (accounting for C soft clip) at
+                      // position 21 + 3 (insertions at position 8)
         { "1S84M2I14M", read, 21,
-            "----------------------cGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGA-GGAGCTCGTTGGTC",
-            insertions3 },
-
+            "-----------------------GAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGA-GGAGCTCGTTGGTC",
+            insertions3 }, // read has 2 insertions accounted for in
+                           // insertions3, 3rd insertion is added as gap at
+                           // position 105
+        { "1S84M2I14M", read, 21,
+            "-----------------------GAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAG---CTC-GTTGGTC",
+            insertions4 }, // 2 insertions in read accounted for at position
+                           // 105; 3 insertions at 109 and 1 insertion at 112
         { "44M1D57M",
         read,
         3,
@@ -59,7 +71,7 @@ public class CigarParserTest
         { "6M2D76M19S",
             "CGAAGCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTCCC",
             4,
-            "---CGAAGC----TTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGAcgaggagctcgttggtccc",
+            "---CGAAGC----TTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGA",
             insertions2 },
 
         { "44M1D57M",
@@ -72,7 +84,7 @@ public class CigarParserTest
             "---CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
             noinsertions },
         { "5S96M", read, 7,
-            "-cgaagCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
+            "------CTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTC",
             noinsertions },
         { "96M5H", read, 7,
             "------CGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAATGGAGGATCAAGTTGGGTTTGGGTTCCGTCCGAACGACGAGGAGCTCGT",
@@ -89,7 +101,7 @@ public class CigarParserTest
     rec.setAlignmentStart(start);
 
     CigarParser cp = new CigarParser('-');
-    String bfresult = cp.parseCigarToSequence(rec, insertions);
+    String bfresult = cp.parseCigarToSequence(rec, insertions, 1);
 
     System.out.println(result);
     System.out.println(bfresult);
@@ -112,10 +124,12 @@ public class CigarParserTest
     builder.addFrag("read_6", 22, 27000, false, false, "2M4I90M5S", "", 0);
     builder.addFrag("read_7", 22, 27000, false, false, "2M1I98M", "", 0);
 
+    builder.addFrag("read_8", 22, 27000, false, false, "3M200N2I5M", "", 0);
+
     Iterator<SAMRecord> it = builder.iterator();
     CigarParser cp = new CigarParser('-');
     SortedMap<Integer, Integer> insertions = cp.getInsertions(it);
-    Assert.assertEquals(insertions.size(), 5);
+    Assert.assertEquals(insertions.size(), 6);
     Assert.assertTrue(insertions.containsKey(28838));
     Assert.assertEquals((int) insertions.get(28838), 1);
     Assert.assertTrue(insertions.containsKey(28885));
@@ -126,5 +140,7 @@ public class CigarParserTest
     Assert.assertEquals((int) insertions.get(28914), 3);
     Assert.assertTrue(insertions.containsKey(27002));
     Assert.assertEquals((int) insertions.get(27002), 4);
+    Assert.assertTrue(insertions.containsKey(27203));
+    Assert.assertEquals((int) insertions.get(27203), 2);
   }
 }