The recent fix for missing calls in single-hypothesis situations would

sometimes consider these as de novo calls, which they aren't.

Author: Lenbok

src/com/rtg/variant/bayes/multisample/family/MendelianAlleleProbabilityDiploidDeNovo.java

@@ -24,7 +24,7 @@ public final class MendelianAlleleProbabilityDiploidDeNovo extends MendelianAlle
   static final int CACHE_SIZE = 101;
   static final double[] CACHED_LOGS = new double[CACHE_SIZE];
   static {
-    for (int i = 0; i < CACHE_SIZE; i++) {
+    for (int i = 1; i < CACHE_SIZE; i++) {
       CACHED_LOGS[i] = Math.log(i);
     }
   }
@@ -131,6 +131,7 @@ private static void setLookup(int fab, int moa, int mob, int cha, int chb, doubl
 
   @Override
   public double probabilityLn(Code code, int father, int mother, int child) {
+    assert code.rangeSize() > 0;
     final UniqueId uid = new UniqueId(code.rangeSize());
     final int fa0 = uid.addId(code.a(father));
     assert fa0 == 0;
@@ -139,7 +140,6 @@ public double probabilityLn(Code code, int father, int mother, int child) {
     final int mo1 = uid.addId(code.bc(mother));
     final int ch0 = uid.addId(code.a(child));
     final int ch1 = uid.addId(code.bc(child));
-    assert code.rangeSize() > 1;
     return LOOKUP[fa1][mo0][mo1][ch0][ch1] - MendelianAlleleProbabilityDiploidDeNovo.cacheLog(code.rangeSize() - 1);
   }
 

src/com/rtg/variant/bayes/multisample/family/MendelianAlleleProbabilityHDDDeNovo.java

@@ -128,7 +128,7 @@ public double probabilityLn(Code code, int father, int mother, int child) {
     final int mo1 = uid.addId(code.bc(mother));
     final int ch0 = uid.addId(code.a(child));
     final int ch1 = uid.addId(code.bc(child));
-    assert code.rangeSize() > 1;
+    assert code.rangeSize() > 0;
     return LOOKUP[mo0][mo1][ch0][ch1] - MendelianAlleleProbabilityDiploidDeNovo.cacheLog(code.rangeSize() - 1);
   }
 

src/com/rtg/variant/bayes/multisample/family/MendelianAlleleProbabilityHDHDeNovo.java

@@ -103,7 +103,7 @@ public double probabilityLn(Code code, int father, int mother, int child) {
     assert mo0 == 0;
     final int mo1 = uid.addId(code.bc(mother));
     final int ch0 = uid.addId(code.a(child));
-    assert code.rangeSize() > 1;
+    assert code.rangeSize() > 0;
     return LOOKUP[mo1][ch0] - MendelianAlleleProbabilityDiploidDeNovo.cacheLog(code.rangeSize() - 1);
   }
 

test/com/rtg/variant/bayes/multisample/family/MendelianAlleleProbabilityDiploidDeNovoTest.java

@@ -21,6 +21,12 @@
  */
 public class MendelianAlleleProbabilityDiploidDeNovoTest extends TestCase {
 
+  public void testUniHypothesisLookup() {
+    // Non de novo should give no likelihood
+    final Code code = new CodeDiploid(1);
+    assertEquals(Double.NEGATIVE_INFINITY, MendelianAlleleProbabilityDiploidDeNovo.SINGLETON.probabilityLn(code, code.code(0), code.code(0), code.code(0)));
+  }
+
   public void testProbabilityLnLookup() {
     final Code code = new CodeDiploid(4);
 

test/com/rtg/variant/bayes/multisample/family/MendelianAlleleProbabilityHDDDeNovoTest.java

@@ -21,6 +21,13 @@
  */
 public class MendelianAlleleProbabilityHDDDeNovoTest extends TestCase {
 
+  public void testUniHypothesisLookup() {
+    // Non de novo should give no likelihood
+    final Code code = new CodeDiploid(1);
+    assertEquals(Double.NEGATIVE_INFINITY, MendelianAlleleProbabilityHDDDeNovo.SINGLETON_HD.probabilityLn(code, code.code(0), code.code(0), code.code(0)));
+  }
+
+
   public void testProbabilityLnLookup() {
     final Code code = new CodeDiploid(4);
 

test/com/rtg/variant/bayes/multisample/family/MendelianAlleleProbabilityHDHDeNovoTest.java

@@ -21,6 +21,12 @@
  */
 public class MendelianAlleleProbabilityHDHDeNovoTest extends TestCase {
 
+  public void testUniHypothesisLookup() {
+    // Non de novo should give no likelihood
+    final Code code = new CodeDiploid(1);
+    assertEquals(Double.NEGATIVE_INFINITY, MendelianAlleleProbabilityHDHDeNovo.SINGLETON_HD.probabilityLn(code, code.code(0), code.code(0), code.code(0)));
+  }
+
   public void testProbabilityLnLookup() {
     final Code code = new CodeDiploid(4);