HTSJDK 4.3.0 for CRAM v3.1 support

.github/workflows/ci.yml

@@ -0,0 +1,31 @@
+name: CI
+
+on:
+  push:
+    branches: ["**"]
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          distribution: temurin
+          java-version: "17"
+          cache: gradle
+      - name: Cache CRAM reference data
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/hts-ref
+          key: hts-ref
+          restore-keys: |
+            hts-ref
+      - name: Run tests
+        run: ./gradlew test

build.gradle

@@ -67,7 +67,7 @@ dependencies {
 
     implementation( group: 'com.beust', name: 'jcommander', version: '1.72' )
 
-    implementation( group: 'com.github.samtools', name: 'htsjdk', version: '4.1.0' )
+    implementation( group: 'com.github.samtools', name: 'htsjdk', version: '4.3.0' )
 
     implementation( "org.jdom:jdom:2.0.2" )
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.7-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

src/test/java/uk/ac/ebi/ena/readtools/sam/CramV31Test.java

@@ -0,0 +1,35 @@
+/*
+ * Copyright 2010-2021 EMBL - European Bioinformatics Institute
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this
+ * file except in compliance with the License. You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software distributed under the
+ * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+ * CONDITIONS OF ANY KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations under the License.
+ */
+package uk.ac.ebi.ena.readtools.sam;
+
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import htsjdk.samtools.ValidationStringency;
+import htsjdk.samtools.cram.ref.ReferenceSource;
+import java.io.File;
+import java.nio.file.Paths;
+import org.junit.Assert;
+import org.junit.Test;
+
+public class CramV31Test {
+  @Test
+  public void cramV31IsReadableWithHtsjdk() throws Exception {
+    File file = Paths.get("src/test/resources/rawreads/18045_1#93.v3.cram").toFile();
+    SamReaderFactory factory = SamReaderFactory.make();
+    factory.validationStringency(ValidationStringency.SILENT);
+    factory.referenceSource(new ReferenceSource((File) null));
+
+    try (SamReader reader = factory.open(file)) {
+      Assert.assertNotNull(reader.getFileHeader());
+      Assert.assertTrue(reader.iterator().hasNext());
+    }
+  }
+}