From cba436fa2f080e968974787d802d32ec9df69c02 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 5 Jan 2011 21:20:26 +0000
Subject: [PATCH] small fix for the table codec; if you see a header line, you
 know you've finished parsing the header.  Also also some changes to return
 the ref ordered data pool test to using MappedStreamSegment instead of
 EntireStream

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4942 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/features/table/TableCodec.java  |  5 ++---
 .../ReferenceOrderedDataPoolUnitTest.java              | 10 ++++++++--
 2 files changed, 10 insertions(+), 5 deletions(-)

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..95d1da5b7 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
@@ -13,7 +13,7 @@ import java.io.IOException;
 import java.util.*;
 
 /**
- * implementation of a simple table (tab or comma delimited format) input files... more improvements to come
+ * implementation of a simple table (tab or comma delimited format) input files
  */
 public class TableCodec implements ReferenceDependentFeatureCodec {
     private String delimiterRegex = "\\s+";
@@ -48,8 +48,6 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
         String[] split = line.split(delimiterRegex);
         if (split.length < 1)
             throw new IllegalArgumentException("TableCodec line = " + line + " doesn't appear to be a valid table format");
-
-
         return new TableFeature(genomeLocParser.parseGenomeLoc(split[0]),Arrays.asList(split),header);
     }
 
@@ -67,6 +65,7 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
                     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);
+                    return header;
                 } else if (!line.startsWith(commentDelimiter)) {
                     break;
                 }
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java
index c720cf4a3..f50734884 100755
--- a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java
@@ -51,6 +51,10 @@ public class ReferenceOrderedDataPoolUnitTest extends BaseTest {
     private GenomeLoc testSite2;
     private GenomeLoc testSite3;
 
+    private GenomeLoc testInterval1; // an interval matching testSite1 -> testSite2 for queries
+    private GenomeLoc testInterval2; // an interval matching testSite2 -> testSite3 for queries
+
+
     @BeforeClass
     public void init() throws FileNotFoundException {
         seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
@@ -59,6 +63,8 @@ public class ReferenceOrderedDataPoolUnitTest extends BaseTest {
         testSite1 = genomeLocParser.createGenomeLoc("chrM",10);
         testSite2 = genomeLocParser.createGenomeLoc("chrM",20);
         testSite3 = genomeLocParser.createGenomeLoc("chrM",30);
+        testInterval1 = genomeLocParser.createGenomeLoc("chrM",10,20);
+        testInterval2 = genomeLocParser.createGenomeLoc("chrM",20,30);
     }
 
     @BeforeMethod
@@ -92,10 +98,10 @@ public class ReferenceOrderedDataPoolUnitTest extends BaseTest {
     @Test
     public void testCreateMultipleIterators() {
         ReferenceOrderedQueryDataPool iteratorPool = new ReferenceOrderedQueryDataPool(triplet,builder,seq.getSequenceDictionary(),genomeLocParser);
-        LocationAwareSeekableRODIterator iterator1 = iteratorPool.iterator( new EntireStream() );
+        LocationAwareSeekableRODIterator iterator1 = iteratorPool.iterator( new MappedStreamSegment(testInterval1) );
 
         // Create a new iterator at position 2.
-        LocationAwareSeekableRODIterator iterator2 = iteratorPool.iterator( new EntireStream() );
+        LocationAwareSeekableRODIterator iterator2 = iteratorPool.iterator( new MappedStreamSegment(testInterval2) );
 
         Assert.assertEquals(iteratorPool.numIterators(), 2, "Number of iterators in the pool is incorrect");
         Assert.assertEquals(iteratorPool.numAvailableIterators(), 0, "Number of available iterators in the pool is incorrect");