Fix output validation

molgenis · Oct 15, 2024 · fc61d96 · fc61d96
1 parent 57328f1
commit fc61d96
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Showing 2 changed files with 14 additions and 7 deletions.
diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/RecordWriterFactoryImpl.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/RecordWriterFactoryImpl.java
@@ -59,30 +59,33 @@ public RecordWriter create(VcfMetadata vcfMetadata, Settings settings) {
     PipedOutputStream pipedOut = new PipedOutputStream();
     Thread writerThread;
     try {
-        writerThread = getWriterThread(pipedOut, writerSettings);
+        writerThread = createWriterThread(pipedOut, writerSettings);
     } catch (IOException e) {
         throw new UncheckedIOException(e);
     }
-    VariantContextWriter vcfWriter = createVcfWriter(writerSettings, pipedOut);
+    VariantContextWriter vcfWriter = createVcfWriter(pipedOut);
     VCFHeader vcfHeader = createHeader(vcfMetadata, settings);
     vcfWriter.writeHeader(vcfHeader);
 
     return new RecordWriterImpl(vcfWriter, writerThread);
   }
 
-  private static VariantContextWriter createVcfWriter(WriterSettings settings, OutputStream outputStream) {
-    Path outputVcfPath = settings.getOutputVcfPath();
-    if (settings.isOverwriteOutput()) {
+  private static Thread createWriterThread(PipedOutputStream pipedOut, WriterSettings writerSettings) throws IOException {
+    Path outputVcfPath = writerSettings.getOutputVcfPath();
+    if (writerSettings.isOverwriteOutput()) {
       try {
         Files.deleteIfExists(outputVcfPath);
       } catch (IOException e) {
         throw new UncheckedIOException(e);
       }
     } else if (Files.exists(outputVcfPath)) {
       throw new IllegalArgumentException(
-          format("cannot create '%s' because it already exists.", outputVcfPath));
+              format("cannot create '%s' because it already exists.", outputVcfPath));
     }
+    return getWriterThread(pipedOut, writerSettings);
+  }
 
+  private static VariantContextWriter createVcfWriter(OutputStream outputStream) {
     return new VariantContextWriterBuilder()
         .clearOptions()
         .setOutputStream(outputStream)

diff --git a/src/main/java/org/molgenis/vcf/decisiontree/runner/VepHelper.java b/src/main/java/org/molgenis/vcf/decisiontree/runner/VepHelper.java
@@ -1,12 +1,15 @@
 package org.molgenis.vcf.decisiontree.runner;
 
+import static java.lang.String.format;
 import static java.util.Collections.singletonList;
 import static org.molgenis.vcf.decisiontree.runner.info.VepMetadataMapperImpl.ALLELE_NUM;
 
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
 
 import java.io.*;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -69,12 +72,13 @@ public static class ModifiedVcfWriter {
         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(settings.getOutputVcfPath().toFile()))) {
+                     BufferedWriter finalWriter = new BufferedWriter(new FileWriter(outputVcfPath.toFile()))) {
 
                     String line;
                     while ((line = reader.readLine()) != null) {