Merge branch 'pvs1-hotfix' into development

exomiser · Sep 20, 2024 · c9af881 · c9af881
2 parents 7d81e85 + e943e04
commit c9af881
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diff --git a/exomiser-cli/CHANGELOG.md b/exomiser-cli/CHANGELOG.md
@@ -1,5 +1,13 @@
 # The Exomiser Command Line Executable - Changelog
 
+## 14.0.2 2024-09-20
+
+- Fix for issue #571. This is a bug-fix release to prevent erroneous assignment of `PVS1` to recessive-compatible variants in LOF-tolerant genes.
+
+## 14.0.1 2024-09-03
+
+- Fix for Issue #565. This is a patch release to prevent a possible ArrayIndexOutOfBoundsException being thrown when outputting the variants TSV file. There are no other changes.
+
 ## 14.0.0 2024-02-29
 
 - Minimum Java version is now **Java 17**

diff --git a/exomiser-cli/pom.xml b/exomiser-cli/pom.xml
@@ -32,7 +32,7 @@
     <parent>
         <groupId>org.monarchinitiative.exomiser</groupId>
         <artifactId>exomiser</artifactId>
-        <version>14.0.0</version>
+        <version>14.0.2</version>
     </parent>
 
 

diff --git a/exomiser-core/CHANGELOG.md b/exomiser-core/CHANGELOG.md
@@ -1,5 +1,13 @@
 # The Exomiser - Core Library Changelog
 
+## 14.0.2 2024-09-20
+
+- Fix for issue #571. This is a bug-fix release to prevent erroneous assignment of `PVS1` to recessive-compatible variants in LOF-tolerant genes.
+
+## 14.0.1 2024-09-03
+
+- Fix for Issue #565. This is a patch release to prevent a possible ArrayIndexOutOfBoundsException being thrown when outputting the variants TSV file. There are no other changes.
+
 ## 14.0.0 2024-02-29
 
 This release **requires data version >= 2402** and **Java version >= 17** (the previous LTS release).

diff --git a/exomiser-core/pom.xml b/exomiser-core/pom.xml
@@ -30,7 +30,7 @@
     <parent>
         <groupId>org.monarchinitiative.exomiser</groupId>
         <artifactId>exomiser</artifactId>
-        <version>14.0.0</version>
+        <version>14.0.2</version>
     </parent>
 
     <dependencies>

diff --git a/...java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java b/...java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java
@@ -237,10 +237,7 @@ private void assignPVS1(AcmgEvidence.Builder acmgEvidenceBuilder, VariantEvaluat
         // Should this be using the hasCompatibleDiseaseMatches variable?
         boolean inGeneWithKnownDiseaseAssociations = !knownDiseases.isEmpty();
         if (inGeneWithKnownDiseaseAssociations && isLossOfFunctionEffect(variantEvaluation.getVariantEffect())
-            && (modeOfInheritance == ModeOfInheritance.ANY
-                || compatibleWithRecessive(modeOfInheritance)
-                || compatibleWithDominant(modeOfInheritance) && (geneContraint != null && geneContraint.isLossOfFunctionIntolerant())
-            )
+            && (geneContraint != null && geneContraint.isLossOfFunctionIntolerant())
         ) {
             if (variantEvaluation.hasTranscriptAnnotations()) {
                 TranscriptAnnotation transcriptAnnotation = variantEvaluation.getTranscriptAnnotations().get(0);

diff --git a/...core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java b/...core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java
@@ -324,7 +324,7 @@ public float maxFreq() {
     @JsonIgnore
     @Nullable
     public Frequency maxFrequency() {
-        return this.size == 0 ? null : frequency(maxSource);
+        return maxSource == -1 ? null : frequency(maxSource);
     }
 
     /**
@@ -454,10 +454,11 @@ public Builder addFrequency(FrequencySource frequencySource, int ac, int an, int
          */
         private Builder addFrequency(FrequencySource frequencySource, float frequency, int ac, int an, int homCount) {
             frequencySources[frequencySource.ordinal()] = frequencySource;
-            frequencyData[frequencySource.ordinal() * WORD_SIZE + FREQ_OFFSET] = frequency;
-            frequencyData[frequencySource.ordinal() * WORD_SIZE + AC_OFFSET] = ac;
-            frequencyData[frequencySource.ordinal() * WORD_SIZE + AN_OFFSET] = an;
-            frequencyData[frequencySource.ordinal() * WORD_SIZE + HOM_OFFSET] = homCount;
+            int freqIndex = frequencySource.ordinal() * WORD_SIZE;
+            frequencyData[freqIndex + FREQ_OFFSET] = frequency;
+            frequencyData[freqIndex + AC_OFFSET] = ac;
+            frequencyData[freqIndex + AN_OFFSET] = an;
+            frequencyData[freqIndex + HOM_OFFSET] = homCount;
             return this;
         }
 
@@ -517,10 +518,12 @@ public FrequencyData build() {
                 FrequencySource source = values[i];
                 if (frequencySources[source.ordinal()] != null) {
                     sources[dataPos] = source;
-                    data[dataPos * WORD_SIZE + FREQ_OFFSET] = frequencyData[source.ordinal() * WORD_SIZE + FREQ_OFFSET];
-                    data[dataPos * WORD_SIZE + AC_OFFSET] = frequencyData[source.ordinal() * WORD_SIZE + AC_OFFSET];
-                    data[dataPos * WORD_SIZE + AN_OFFSET] = frequencyData[source.ordinal() * WORD_SIZE + AN_OFFSET];
-                    data[dataPos * WORD_SIZE + HOM_OFFSET] = frequencyData[source.ordinal() * WORD_SIZE + HOM_OFFSET];
+                    int dataIndex = dataPos * WORD_SIZE;
+                    int freqIndex = source.ordinal() * WORD_SIZE;
+                    data[dataIndex + FREQ_OFFSET] = frequencyData[freqIndex + FREQ_OFFSET];
+                    data[dataIndex + AC_OFFSET] = frequencyData[freqIndex + AC_OFFSET];
+                    data[dataIndex + AN_OFFSET] = frequencyData[freqIndex + AN_OFFSET];
+                    data[dataIndex + HOM_OFFSET] = frequencyData[freqIndex + HOM_OFFSET];
                     dataPos++;
                 }
             }

diff --git a/.../org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssignerTest.java b/.../org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssignerTest.java
@@ -103,7 +103,7 @@ void testAssignsPVS1() {
 
             "MALE, X_RECESSIVE, X_RECESSIVE, true",
             "FEMALE, X_RECESSIVE, X_RECESSIVE, true",
-            "UNKNOWN, X_RECESSIVE, X_RECESSIVE, false",
+            "UNKNOWN, X_RECESSIVE, X_RECESSIVE, true",
 
             "MALE, X_DOMINANT, X_DOMINANT, true",
             "FEMALE, X_DOMINANT, X_DOMINANT, true",

diff --git a/.../src/test/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyDataTest.java b/.../src/test/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyDataTest.java
@@ -26,12 +26,15 @@
 
 package org.monarchinitiative.exomiser.core.model.frequency;
 
+import org.h2.mvstore.MVStore;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
+import org.monarchinitiative.exomiser.core.genome.dao.serialisers.MvStoreUtil;
+import org.monarchinitiative.exomiser.core.model.AlleleProtoAdaptor;
+import org.monarchinitiative.exomiser.core.proto.AlleleProto;
+import org.monarchinitiative.exomiser.core.proto.AlleleProtoFormatter;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
 
 import static org.hamcrest.CoreMatchers.equalTo;
 import static org.hamcrest.CoreMatchers.is;
@@ -287,6 +290,17 @@ public void testGetMaxFrequencyWithData() {
         assertThat(instance.maxFrequency(), equalTo(maxFrequency));
     }
 
+    @Test
+    public void testGetMaxFrequencyWhenZeroData() {
+        Frequency maxFrequency = Frequency.of(GNOMAD_E_AFR, 0, 1000, 0);
+        Frequency minFrequency = Frequency.of(TOPMED, 0f);
+        FrequencyData instance = FrequencyData.of("rs545662810", minFrequency, maxFrequency);
+
+        assertThat(instance.maxFrequency(), equalTo(null));
+        assertThat(instance.maxFreq(), equalTo(0f));
+        assertThat(instance.frequencies(), equalTo(List.of(minFrequency, maxFrequency)));
+    }
+
     @Test
     public void testHasFrequencyOverPercentageValue() {
         float maxFreq = 0.05f;
@@ -482,12 +496,12 @@ void floatArray() {
         var an = 10000;
         var hom = 10;
         var af = Frequency.percentageFrequency(ac, an);
-        System.out.println("AF=" + af);
+
         data[0] = (float) ac;
         data[1] = (float) an;
         data[2] = (float) hom;
         data[3] = (float) af;
-        System.out.println("dataAF=" + data[3]);
+
         assertThat(Frequency.percentageFrequency((int) data[0], (int) data[1]), equalTo((float) data[3]));
     }
 

diff --git a/exomiser-data-genome/pom.xml b/exomiser-data-genome/pom.xml
@@ -31,7 +31,7 @@
     <parent>
         <groupId>org.monarchinitiative.exomiser</groupId>
         <artifactId>exomiser</artifactId>
-        <version>14.0.0</version>
+        <version>14.0.2</version>
     </parent>
 
     <dependencies>

diff --git a/exomiser-data-phenotype/pom.xml b/exomiser-data-phenotype/pom.xml
@@ -31,7 +31,7 @@
     <parent>
         <groupId>org.monarchinitiative.exomiser</groupId>
         <artifactId>exomiser</artifactId>
-        <version>14.0.0</version>
+        <version>14.0.2</version>
     </parent>
 
     <properties>

diff --git a/exomiser-rest-prioritiser/pom.xml b/exomiser-rest-prioritiser/pom.xml
@@ -27,7 +27,7 @@
     <parent>
         <groupId>org.monarchinitiative.exomiser</groupId>
         <artifactId>exomiser</artifactId>
-        <version>14.0.0</version>
+        <version>14.0.2</version>
     </parent>
 
     <artifactId>exomiser-rest-prioritiser</artifactId>

diff --git a/exomiser-spring-boot-autoconfigure/pom.xml b/exomiser-spring-boot-autoconfigure/pom.xml
@@ -35,7 +35,7 @@
     <parent>
         <groupId>org.monarchinitiative.exomiser</groupId>
         <artifactId>exomiser</artifactId>
-        <version>14.0.0</version>
+        <version>14.0.2</version>
     </parent>
 
     <dependencies>

diff --git a/exomiser-spring-boot-starter/pom.xml b/exomiser-spring-boot-starter/pom.xml
@@ -28,7 +28,7 @@
     <parent>
         <groupId>org.monarchinitiative.exomiser</groupId>
         <artifactId>exomiser</artifactId>
-        <version>14.0.0</version>
+        <version>14.0.2</version>
     </parent>
 
     <artifactId>exomiser-spring-boot-starter</artifactId>

diff --git a/exomiser-spring-boot-test/pom.xml b/exomiser-spring-boot-test/pom.xml
@@ -27,7 +27,7 @@
     <parent>
         <groupId>org.monarchinitiative.exomiser</groupId>
         <artifactId>exomiser</artifactId>
-        <version>14.0.0</version>
+        <version>14.0.2</version>
     </parent>
 
     <artifactId>exomiser-spring-boot-test</artifactId>

diff --git a/exomiser-web/pom.xml b/exomiser-web/pom.xml
@@ -31,7 +31,7 @@
     <parent>
         <groupId>org.monarchinitiative.exomiser</groupId>
         <artifactId>exomiser</artifactId>
-        <version>14.0.0</version>
+        <version>14.0.2</version>
     </parent>
 
     <properties>

diff --git a/phenix-repository/pom.xml b/phenix-repository/pom.xml
@@ -7,7 +7,7 @@
     <parent>
         <groupId>org.monarchinitiative.exomiser</groupId>
         <artifactId>exomiser</artifactId>
-        <version>14.0.0</version>
+        <version>14.0.2</version>
     </parent>
 
     <artifactId>phenix-repository</artifactId>

diff --git a/pom.xml b/pom.xml
@@ -24,7 +24,7 @@
 
     <groupId>org.monarchinitiative.exomiser</groupId>
     <artifactId>exomiser</artifactId>
-    <version>14.0.0</version>
+    <version>14.0.2</version>
     <packaging>pom</packaging>
 
     <name>exomiser</name>