From 5d6aad67e2c2565ad948a41aff2d6e07208ea2fd Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Sun, 7 Oct 2012 00:01:27 -0400
Subject: [PATCH] Fix for bug reported on forums: VariantsToTable does not
 handle lists and nested arrays correctly.  Added an integration test to cover
 printing of PLs.

---
 .../walkers/variantutils/VariantsToTable.java | 25 +++++++++++++++++--
 .../VariantsToTableIntegrationTest.java       | 15 ++++++++++-
 2 files changed, 37 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index b9577ca9b..dd5264a1b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -42,6 +42,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.PrintStream;
+import java.lang.reflect.Array;
 import java.util.*;
 
 /**
@@ -334,12 +335,12 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
         return records;
     }
 
-    private static void addFieldValue(Object val, List<List<String>> result) {
+    private static void addFieldValue(final Object val, final List<List<String>> result) {
         final int numResultRecords = result.size();
         
         // if we're trying to create a single output record, add it
         if ( numResultRecords == 1 ) {
-            result.get(0).add(val.toString());
+            result.get(0).add(prettyPrintObject(val));
         }
         // if this field is a list of the proper size, add the appropriate entry to each record
         else if ( (val instanceof List) && ((List)val).size() == numResultRecords ) {
@@ -355,6 +356,26 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
         }
     }
 
+    private static String prettyPrintObject(final Object val) {
+        if ( val instanceof List )
+            return prettyPrintObject(((List)val).toArray());
+
+        if ( !val.getClass().isArray() )
+            return val.toString();
+
+        final int length = Array.getLength(val);
+        if ( length == 0 )
+            return "";
+
+        final StringBuilder sb = new StringBuilder(prettyPrintObject(Array.get(val, 0)));
+        for ( int i = 1; i < length; i++ ) {
+            sb.append(",");
+            sb.append(prettyPrintObject(Array.get(val, i)));
+        }
+        return sb.toString();
+    }
+
+
     public static List<List<String>> extractFields(VariantContext vc, List<String> fields, boolean allowMissingData) {
         return extractFields(vc, fields, null, null, allowMissingData, false);
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java
index 2ffcd02e2..8186ffc7d 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java
@@ -63,7 +63,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
     @Test(enabled = true)
     public void testMultiAllelicOneRecord() {
         WalkerTestSpec spec = new WalkerTestSpec(variantsToTableMultiAllelicCmd(""),
-                Arrays.asList("13dd36c08be6c800f23988e6000d963e"));
+                Arrays.asList("0ff49c08690f61a38614606a090f23ea"));
         executeTest("testMultiAllelicOneRecord", spec);
     }
 
@@ -100,6 +100,19 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
         executeTest("testGenotypeFieldsWithInline", spec);
     }
 
+    @Test(enabled = true)
+    public void testListFields() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-R " + b36KGReference +
+                        " --variant " + privateTestDir + "vcfexample.withMLE.vcf" +
+                        " -T VariantsToTable" +
+                        " -GF PL" +
+                        " -o %s",
+                1,
+                Arrays.asList("1cb2737ab0eaee0a9ae25ab2e7ac3e7e"));
+        executeTest("testGenotypeFields", spec);
+    }
+
     @Test(enabled = true)
     public void testMoltenOutput() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(