VariantsToTable: setting default to include all fields

Fixes #7677
broadinstitute · Jun 17, 2022 · f20763f · f20763f
1 parent d22b752
commit f20763f
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Showing 2 changed files with 26 additions and 1 deletion.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable.java
@@ -12,7 +12,6 @@
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
-import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
 import picard.cmdline.programgroups.VariantEvaluationProgramGroup;
 import org.broadinstitute.hellbender.engine.FeatureContext;
 import org.broadinstitute.hellbender.engine.ReadsContext;
@@ -30,6 +29,7 @@
 import java.util.function.Function;
 
 import static org.broadinstitute.hellbender.utils.Utils.split;
+import static org.broadinstitute.hellbender.utils.Utils.stream;
 
 /**
  * Extract fields from a VCF file to a tab-delimited table
@@ -135,6 +135,10 @@ public final class VariantsToTable extends VariantWalker {
             shortName="F",
             doc="The name of a standard VCF field or an INFO field to include in the output table", optional=true)
     protected List<String> fieldsToTake = new ArrayList<>();
+    //protected List<String> fieldsToTake = VCFHeader.HEADER_FIELDS.name();
+
+
+
 
     /**
      * Any annotation name in the FORMAT field (e.g., GQ, PL) to include in the output table.
@@ -238,6 +242,14 @@ public void onTraversalStart() {
             outputStream.println("RecordID\tSample\tVariable\tValue");
         } else {
             final List<String> fields = new ArrayList<>();
+
+            // if no fields specified, default to all mandatory fields
+            if(fieldsToTake.isEmpty()){
+                for(VCFHeader.HEADER_FIELDS header : VCFHeader.HEADER_FIELDS.values()){
+                    fieldsToTake.add(header.name());
+                }
+            }
+
             fields.addAll(fieldsToTake);
             fields.addAll(asFieldsToTake);
             fields.addAll(createGenotypeFields());

diff --git a/.../broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java b/.../broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java
@@ -5,6 +5,7 @@
 import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
 import org.testng.annotations.Test;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.Arrays;
 
@@ -236,4 +237,16 @@ public void testMoltenOutputWithMultipleAlleles() throws IOException {
         spec.setTrimWhiteSpace(false);
         spec.executeTest("testMoltenOutputWithMultipleAlleles", this);
     }
+
+    @Test
+    public void testNoFieldsSpecified() throws IOException {
+        final File inputFile = new File(getToolTestDataDir(), "multiallelic.vcf");
+        final File outputFile = new File(getToolTestDataDir(), "noFieldsOutput.vcf");
+        //createTempFile("noFieldsOutput", ".table");
+
+        final String[] args = new String[] {"--variant", inputFile.getAbsolutePath(),
+                "-O", outputFile.getAbsolutePath()};
+        runCommandLine(args);
+    }
+
 }