Merge pull request #786 from broadinstitute/pd_variantstotable_sma

Fix VariantsToTable output of FORMAT record lists when -SMA is specified

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(

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java

@@ -351,7 +351,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
         }
         // otherwise, add the original value to all of the records
         else {
-            final String valStr = val.toString();
+            final String valStr = prettyPrintObject(val);
             for ( List<String> record : result )
                 record.add(valStr);
         }