Improve test coverage + fix warnings

src/main/java/org/molgenis/vcf/decisiontree/filter/RecordWriterImpl.java

@@ -25,7 +25,7 @@ public void close() {
           writerThread.join();
       } catch (InterruptedException e) {
           writerThread.interrupt();
-          throw new RuntimeException(e);
+          throw new WriterThreadInterruptedException(e.getMessage());
       }
   }
 }

src/main/java/org/molgenis/vcf/decisiontree/filter/WriterThreadInterruptedException.java

@@ -0,0 +1,13 @@
+package org.molgenis.vcf.decisiontree.filter;
+
+import java.io.Serial;
+import static java.lang.String.format;
+
+public class WriterThreadInterruptedException extends RuntimeException {
+    @Serial
+    private static final long serialVersionUID = 1L;
+
+    public WriterThreadInterruptedException(String message) {
+        super(format("VCF writer was interrupted with message: %s", message));
+    }
+}

src/main/java/org/molgenis/vcf/decisiontree/runner/InvalidVcfLineException.java

@@ -7,6 +7,7 @@
 public class InvalidVcfLineException extends RuntimeException {
     @Serial
     private static final long serialVersionUID = 1L;
+
     public InvalidVcfLineException(String line) {
         super(
                 format(

src/main/java/org/molgenis/vcf/decisiontree/runner/ModifiedVcfWriter.java

@@ -0,0 +1,40 @@
+package org.molgenis.vcf.decisiontree.runner;
+
+import org.molgenis.vcf.decisiontree.WriterSettings;
+
+import java.io.*;
+import java.nio.file.Path;
+
+public class ModifiedVcfWriter {
+    public static final String CNV_TR = "<CNV:TR>";
+    public static final String PATTERN = "<CNV:TR\\d+>";
+
+    private ModifiedVcfWriter() {
+    }
+
+    public static Thread getWriterThread(PipedOutputStream pipedOut, WriterSettings settings) throws IOException {
+        Path outputVcfPath = settings.getOutputVcfPath();
+        PipedInputStream pipedIn = new PipedInputStream(pipedOut);
+
+        // Create a thread to write the modified output to a file
+        Thread writerThread = new Thread(() -> {
+            try (BufferedReader reader = new BufferedReader(new InputStreamReader(pipedIn));
+                 BufferedWriter finalWriter = new BufferedWriter(new FileWriter(outputVcfPath.toFile()))) {
+
+                String line;
+                while ((line = reader.readLine()) != null) {
+                    String modifiedContent = line.replaceAll(PATTERN, CNV_TR);
+
+                    finalWriter.write(modifiedContent);
+                    finalWriter.newLine();
+                }
+
+            } catch (IOException ioException) {
+                throw new UncheckedIOException(ioException);
+            }
+        });
+
+        writerThread.start();
+        return writerThread;
+    }
+}

src/main/java/org/molgenis/vcf/decisiontree/runner/RecordWriterFactoryImpl.java

@@ -1,10 +1,10 @@
 package org.molgenis.vcf.decisiontree.runner;
 
 import static java.lang.String.format;
-import static org.molgenis.vcf.decisiontree.runner.VepHelper.ModifiedVcfWriter.getWriterThread;
 import static org.molgenis.vcf.decisiontree.filter.SampleAnnotatorImpl.VIPC_S;
 import static org.molgenis.vcf.decisiontree.filter.SampleAnnotatorImpl.VIPP_S;
 import static org.molgenis.vcf.decisiontree.filter.SampleAnnotatorImpl.VIPL_S;
+import static org.molgenis.vcf.decisiontree.runner.ModifiedVcfWriter.getWriterThread;
 import static org.molgenis.vcf.utils.utils.HeaderUtils.fixVcfFilterHeaderLines;
 import static org.molgenis.vcf.utils.utils.HeaderUtils.fixVcfFormatHeaderLines;
 import static org.molgenis.vcf.utils.utils.HeaderUtils.fixVcfInfoHeaderLines;

src/main/java/org/molgenis/vcf/decisiontree/runner/VepHelper.java

@@ -6,14 +6,11 @@
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
 
-import java.io.*;
-import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import org.apache.logging.log4j.util.Strings;
-import org.molgenis.vcf.decisiontree.WriterSettings;
 import org.molgenis.vcf.decisiontree.filter.UnknownFieldException;
 import org.molgenis.vcf.decisiontree.filter.VcfRecord;
 import org.molgenis.vcf.decisiontree.filter.model.FieldType;
@@ -62,37 +59,4 @@ public VcfRecord createEmptyCsqRecord(VcfRecord vcfRecord,
         singletonList(Strings.join(values, '|')));
     return new VcfRecord(variantContextBuilder.make());
   }
-
-    public static class ModifiedVcfWriter {
-        public static final String CNV_TR = "<CNV:TR>";
-        public static final String PATTERN = "<CNV:TR\\d+>";
-
-        private ModifiedVcfWriter(){}
-
-        public static Thread getWriterThread(PipedOutputStream pipedOut, WriterSettings settings) throws IOException {
-            Path outputVcfPath = settings.getOutputVcfPath();
-            PipedInputStream pipedIn = new PipedInputStream(pipedOut);
-
-            // Create a thread to write the modified output to a file
-            Thread writerThread = new Thread(() -> {
-                try (BufferedReader reader = new BufferedReader(new InputStreamReader(pipedIn));
-                     BufferedWriter finalWriter = new BufferedWriter(new FileWriter(outputVcfPath.toFile()))) {
-
-                    String line;
-                    while ((line = reader.readLine()) != null) {
-                        String modifiedContent = line.replaceAll(PATTERN, CNV_TR);
-
-                        finalWriter.write(modifiedContent);
-                        finalWriter.newLine();
-                    }
-
-                } catch (IOException ioException) {
-                    throw new UncheckedIOException(ioException);
-                }
-            });
-
-            writerThread.start();
-            return writerThread;
-        }
-    }
 }

src/test/java/org/molgenis/vcf/decisiontree/filter/WriterThreadInterruptedExceptionTest.java

@@ -0,0 +1,15 @@
+package org.molgenis.vcf.decisiontree.filter;
+
+import org.junit.jupiter.api.Test;
+import static org.junit.jupiter.api.Assertions.*;
+
+class WriterThreadInterruptedExceptionTest {
+
+    @Test
+    void getMessage() {
+        assertEquals(
+                "VCF writer was interrupted with message: I don't want to interrupt, but ...",
+                new WriterThreadInterruptedException(
+                        "I don't want to interrupt, but ...").getMessage());
+    }
+}