Merge branch 'splice-acmg' into development

# Conflicts: # exomiser-cli/pom.xml # exomiser-core/pom.xml # exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java # exomiser-data-genome/pom.xml # exomiser-data-phenotype/pom.xml # exomiser-rest-prioritiser/pom.xml # exomiser-spring-boot-autoconfigure/pom.xml # exomiser-spring-boot-starter/pom.xml # exomiser-spring-boot-test/pom.xml # exomiser-web/pom.xml # phenix-repository/pom.xml # pom.xml
exomiser · Nov 13, 2024 · 70802e4 · 70802e4
2 parents c9af881 + a1720b2
commit 70802e4
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,4 +1,4 @@
-version: 2
+version: 2.1
 jobs:
   build:
     working_directory: ~/exomiser
@@ -11,7 +11,9 @@ jobs:
       - image: cimg/openjdk:17.0.7
     steps:
       - checkout
-      - run: chmod +x mvnw
+      - run:
+          name: make executable
+          command: chmod +x mvnw
       - restore_cache:
           key: exomiser-{{ arch }}-{{ checksum "pom.xml" }}
       - run: ./mvnw clean install -Dmaven.javadoc.skip=true -B -V

diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -20,9 +20,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up JDK 17
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         java-version: '17'
         distribution: 'temurin'

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>14.0.2</version>
+        <version>14.1.0-ALPHA</version>
     </parent>
 
 

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>14.0.2</version>
+        <version>14.1.0-ALPHA</version>
     </parent>
 
     <dependencies>
@@ -139,6 +139,12 @@
             <groupId>jakarta.annotation</groupId>
             <artifactId>jakarta.annotation-api</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.rocksdb</groupId>
+            <artifactId>rocksdbjni</artifactId>
+            <version>7.6.0</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>

diff --git a/.../main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acgs2020Classifier.java b/.../main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acgs2020Classifier.java
@@ -29,8 +29,10 @@
  * Implementation of the ACGS v4 guidelines, Table 3 from
  * https://www.acgs.uk.com/media/11631/uk-practice-guidelines-for-variant-classification-v4-01-2020.pdf
  *
+ * @deprecated Guidelines now suggest using the {@link Acmg2020PointsBasedClassifier}
  * @since 13.1.0
  */
+@Deprecated(since = "14.1.0", forRemoval = true)
 public final class Acgs2020Classifier implements AcmgEvidenceClassifier {
 
     public AcmgClassification classify(AcmgEvidence acmgEvidence) {

diff --git a/.../main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015Classifier.java b/.../main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015Classifier.java
@@ -29,8 +29,10 @@
  * Implementation of the 2015 ACMG Standards guidelines for interpretation of sequence variants (Richards et al. doi:10.1038/gim.2015.30).
  * Table 5 'Rules for combining criteria to classify sequence variants'
  *
+ * @deprecated Guidelines now suggest using the {@link Acmg2020PointsBasedClassifier}
  * @since 13.1.0
  */
+@Deprecated(since = "14.1.0", forRemoval = true)
 public final class Acmg2015Classifier implements AcmgEvidenceClassifier {
 
     public AcmgClassification classify(AcmgEvidence acmgEvidence) {

diff --git a/...java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java b/...java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java
diff --git a/...e/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgCriterion.java b/...e/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgCriterion.java
@@ -79,12 +79,12 @@ public static Evidence parseValue(String displayString) {
             } catch (IllegalArgumentException ex) {
                 // swallow and try the display string
             }
-            return switch (displayString) {
-                case "StandAlone" -> STAND_ALONE;
-                case "VeryStrong" -> VERY_STRONG;
-                case "Strong" -> STRONG;
-                case "Moderate" -> MODERATE;
-                case "Supporting" -> SUPPORTING;
+            return switch (displayString.toLowerCase()) {
+                case "standalone" -> STAND_ALONE;
+                case "verystrong" -> VERY_STRONG;
+                case "strong" -> STRONG;
+                case "moderate" -> MODERATE;
+                case "supporting" -> SUPPORTING;
                 default -> throw new IllegalArgumentException("Unrecognised evidence value '" + displayString + "'");
             };
         }

diff --git a/...re/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidence.java b/...re/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/AcmgEvidence.java
@@ -246,6 +246,24 @@ public String toString() {
         return '[' + stringJoiner.toString() + ']';
     }
 
+    public static AcmgEvidence parseAcmgEvidence(String criteria) {
+        if (criteria == null || criteria.isEmpty()) {
+            return AcmgEvidence.empty();
+        }
+        AcmgEvidence.Builder acmgEvidenceBuilder = AcmgEvidence.builder();
+        for (String criterion : criteria.replace("[", "").replace("]", "").split("[, ]+")) {
+            String[] criteriaModifier = criterion.trim().split("_");
+            AcmgCriterion acmgCriterion = AcmgCriterion.valueOf(criteriaModifier[0]);
+            if (criteriaModifier.length == 2) {
+                AcmgCriterion.Evidence modifier = AcmgCriterion.Evidence.parseValue(criteriaModifier[1]);
+                acmgEvidenceBuilder.add(acmgCriterion, modifier);
+            } else {
+                acmgEvidenceBuilder.add(acmgCriterion);
+            }
+        }
+        return acmgEvidenceBuilder.build();
+    }
+
     public static class Builder {
 
         private final EnumMap<AcmgCriterion, Evidence> evidence = new EnumMap<>(AcmgCriterion.class);
@@ -264,6 +282,19 @@ public boolean contains(AcmgCriterion acmgCriterion) {
             return evidence.containsKey(acmgCriterion);
         }
 
+        public boolean containsWithEvidence(AcmgCriterion acmgCriterion, Evidence evidenceStrength) {
+            return evidence.containsKey(acmgCriterion) && evidence.get(acmgCriterion) == evidenceStrength;
+        }
+
+        public void remove(AcmgCriterion acmgCriterion) {
+            evidence.remove(acmgCriterion);
+        }
+
+        @Nullable
+        public Evidence evidenceForCategory(AcmgCriterion acmgCriterion) {
+            return evidence.get(acmgCriterion);
+        }
+
         public AcmgEvidence build() {
             return evidence.isEmpty() ? EMPTY : new AcmgEvidence(evidence);
         }