From b9cb57f4b9ba5cb3f40d87ee8960966a7cbccf55 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 31 Dec 2010 16:35:04 +0000
Subject: [PATCH] A unit test is failing on bamboo in a way I can't reproduce
 (or even explain). Checking in some debugging info.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4916 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/features/table/TableCodec.java       | 3 +++
 .../datasources/providers/ReferenceOrderedViewUnitTest.java | 6 ++++++
 2 files changed, 9 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
index a930e825f..84e770fa1 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
@@ -60,10 +60,13 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
 
     @Override
     public Object readHeader(LineReader reader) {
+        System.out.printf("  TableCodec.readHeader:%n  ");
+        new Exception().printStackTrace(System.out);
         String line = "";
         try {
             while ((line = reader.readLine()) != null) {
                 if (line.startsWith(headerDelimiter)) {
+                    System.out.printf("  Line w/ header delimiter: %s%n",line);
                     if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines.  The second is = " + line);
                     String spl[] = line.split(delimiterRegex);
                     for (String s : spl) header.add(s);
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
index 0ab804eb9..24ef12525 100755
--- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
@@ -64,12 +64,14 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
      */
     @Test
     public void testNoBindings() {
+        System.out.printf("Starting testNoBindings%n");
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));
         LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Collections.<ReferenceOrderedDataSource>emptyList());
         ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
 
         RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",10));
         Assert.assertEquals(tracker.getAllRods().size(), 0, "The tracker should not have produced any data");
+        System.out.printf("Ending testNoBindings%n");
     }
 
     /**
@@ -77,6 +79,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
      */
     @Test
     public void testSingleBinding() {
+        System.out.printf("Starting testSingleBinding%n");
         String fileName = testDir + "TabularDataTest.dat";
         RMDTriplet triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE);
         ReferenceOrderedDataSource dataSource = new ReferenceOrderedDataSource(triplet,builder,seq.getSequenceDictionary(),genomeLocParser,false);
@@ -92,6 +95,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
         Assert.assertEquals(datum.get("COL1"),"C","datum parameter for COL1 is incorrect");
         Assert.assertEquals(datum.get("COL2"),"D","datum parameter for COL2 is incorrect");
         Assert.assertEquals(datum.get("COL3"),"E","datum parameter for COL3 is incorrect");
+        System.out.printf("Ending testSingleBinding%n");
     }
 
     /**
@@ -99,6 +103,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
      */
     @Test
     public void testMultipleBinding() {
+        System.out.printf("Starting testMultipleBinding%n");
         File file = new File(testDir + "TabularDataTest.dat");
 
         RMDTriplet testTriplet1 = new RMDTriplet("tableTest1","Table",file.getAbsolutePath(),RMDStorageType.FILE);
@@ -124,5 +129,6 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
         Assert.assertEquals(datum2.get("COL1"),"C","datum2 parameter for COL1 is incorrect");
         Assert.assertEquals(datum2.get("COL2"),"D","datum2 parameter for COL2 is incorrect");
         Assert.assertEquals(datum2.get("COL3"),"E","datum2 parameter for COL3 is incorrect");
+        System.out.printf("Ending testMultipleBinding%n");
     }
 }