Add a --numeric-gt option to VariantsToTable

* add an new option to VariantsToTable to allow output VCF style numeric GT fields
previously it always output the actual bases of the Allele in the GT spot
* resolves #8160
* updates htsjdk to 3.0.5

src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.tools.walkers.variantutils;
 
 import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.*;
 import org.apache.logging.log4j.LogManager;
@@ -122,6 +123,7 @@
 public final class VariantsToTable extends VariantWalker {
     public final static String SPLIT_MULTI_ALLELIC_LONG_NAME = "split-multi-allelic";
     public final static String SPLIT_MULTI_ALLELIC_SHORT_NAME = "SMA";
+    public static final String NUMERIC_GT_FULLNAME = "numeric-gt";
 
     static final Logger logger = LogManager.getLogger(VariantsToTable.class);
 
@@ -204,6 +206,11 @@ public final class VariantsToTable extends VariantWalker {
             doc="Fail on missing data", optional=true)
     public boolean errorIfMissingData = false;
 
+    @Argument(fullName = NUMERIC_GT_FULLNAME,
+              doc = "write the GT field the way it appears in a VCF ( ex. 0/1 instead of A/T )",
+              optional = true)
+    public boolean useNumericGT = false;
+
     private static final String MISSING_DATA = "NA";
 
     private SortedSet<String> samples;
@@ -341,7 +348,7 @@ private void emitMoltenizedOutput(final List<String> record) {
      * @param vc                the VariantContext whose field values we can to capture
      * @return List of lists of field values
      */
-    protected List<List<String>> extractFields(final VariantContext vc) {
+    private List<List<String>> extractFields(final VariantContext vc) {
 
         final int numRecordsToProduce = splitMultiAllelic ? vc.getAlternateAlleles().size() : 1;
         final List<List<String>> records = new ArrayList<>(numRecordsToProduce);
@@ -395,18 +402,23 @@ protected List<List<String>> extractFields(final VariantContext vc) {
 
     private void addGenotypeFieldsToRecords(final VariantContext vc, final List<List<String>> records, final boolean errorIfMissingData) {
         for ( final String sample : samples ) {
+            final Genotype genotype = vc.getGenotype(sample);
             for ( final String gf : genotypeFieldsToTake ) {
-                if ( vc.hasGenotype(sample) && vc.getGenotype(sample).hasAnyAttribute(gf) ) {
+                if ( vc.hasGenotype(sample) && genotype.hasAnyAttribute(gf) ) {
                     if (VCFConstants.GENOTYPE_KEY.equals(gf)) {
-                        addFieldValue(vc.getGenotype(sample).getGenotypeString(true), records);
+                        if(useNumericGT) {
+                            addFieldValue(VCFEncoder.encodeGtField(vc, genotype), records);
+                        } else {
+                            addFieldValue(genotype.getGenotypeString(true), records);
+                        }
                     } else {
                         /**
                          * TODO - If gf == "FT" and the GT record is not filtered, Genotype.getAnyAttribute == null. Genotype.hasAnyAttribute should be changed so it
                          * returns false for this condition. Presently, it always returns true. Once this is fixed, then only the "addFieldValue" statement will
                          * remain in the following logic block.
                          */
-                        if (vc.getGenotype(sample).getAnyAttribute(gf) != null) {
-                            addFieldValue(vc.getGenotype(sample).getAnyAttribute(gf), records);
+                        if (genotype.getAnyAttribute(gf) != null) {
+                            addFieldValue(genotype.getAnyAttribute(gf), records);
                         } else {
                             handleMissingData(errorIfMissingData, gf, records, vc);
                         }                    }
@@ -416,21 +428,21 @@ private void addGenotypeFieldsToRecords(final VariantContext vc, final List<List
             }
 
             for ( final String field : asGenotypeFieldsToTake) {
-                if ( vc.hasGenotype(sample) && vc.getGenotype(sample).hasAnyAttribute(field) ) {
+                if ( vc.hasGenotype(sample) && genotype.hasAnyAttribute(field) ) {
                     if (splitMultiAllelic) {
                         if (VCFConstants.GENOTYPE_ALLELE_DEPTHS.equals(field)) {
-                            List<String> altDepths = new ArrayList<>();
-                            int[] allDepths = vc.getGenotype(sample).getAD();
+                            final List<String> altDepths = new ArrayList<>();
+                            int[] allDepths = genotype.getAD();
                             for (int i = 1; i < allDepths.length; i++) {
                                 altDepths.add(allDepths[0] + "," + allDepths[i]);
                             }
                             addFieldValue(altDepths, records);
                         } else {
-                            addAlleleSpecificFieldValue(split(vc.getGenotype(sample).getExtendedAttribute(field).toString(), ','),
+                            addAlleleSpecificFieldValue(split(genotype.getExtendedAttribute(field).toString(), ','),
                                     records, inputHeader.getFormatHeaderLine(field).getCountType());
                         }
                     } else {
-                        final String value = vc.getGenotype(sample).getAnyAttribute(field).toString();
+                        final String value = genotype.getAnyAttribute(field).toString();
                         if (field.equals(VCFConstants.GENOTYPE_ALLELE_DEPTHS)) {
                             addFieldValue(value.replace("[","").replace("]","").replaceAll("\\s",""),records);
                         } else {

src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java

@@ -2,6 +2,7 @@
 
 import org.broadinstitute.hellbender.CommandLineProgramTest;
 import org.broadinstitute.hellbender.exceptions.UserException;
+import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
 import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
 import org.testng.annotations.Test;
 
@@ -276,5 +277,20 @@ public void testNoFieldsSpecifiedFormatFieldInHeaderNoSamples() throws IOExcepti
 
         IntegrationTestSpec.assertEqualTextFiles(outputFile, expectedFile);
     }
+
+    @Test
+    public void testNumericGTFlag() throws IOException {
+        final File inputFile = new File(getToolTestDataDir(), "VCFWithGenotypes_1000G.phase3.snippet.vcf");
+        final File outputFile = createTempFile("numericGT", ".table");
+        final File expectedFile = new File(getToolTestDataDir(), "expected.numericGT.table");
+
+        final ArgumentsBuilder args = new ArgumentsBuilder();
+        args.addVCF(inputFile)
+                        .addOutput(outputFile)
+                        .addFlag(VariantsToTable.NUMERIC_GT_FULLNAME);
+        runCommandLine(args);
+
+        IntegrationTestSpec.assertEqualTextFiles(outputFile, expectedFile);
+    }
 
 }