diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java index ebda9e23e..fd7cf737a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java @@ -114,6 +114,21 @@ public class VariantsToTableIntegrationTest extends WalkerTest { executeTest("testGenotypeFields", spec); } + @Test + public void testMultiallelicGenotypeFields() { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + "-R " + b37KGReference + + " --variant " + privateTestDir + "multiallelic_gt.vcf" + + " -T VariantsToTable" + + " -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F MULTI-ALLELIC" + + " -GF PL -GF AD" + + " -SMA" + + " -o %s", + 1, + Arrays.asList("7d38e7adb07eee94405188d145f22bb5")); + executeTest("testMultiallelicGenotypeFields", spec); + } + @Test(enabled = true) public void testGenotypeFieldsWithInline() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java index 62845501b..081403f35 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java @@ -351,7 +351,7 @@ public class VariantsToTable extends RodWalker { } // otherwise, add the original value to all of the records else { - final String valStr = val.toString(); + final String valStr = prettyPrintObject(val); for ( List record : result ) record.add(valStr); }