From 0a16519aa2591050e28a3dd871664cf9844a0207 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 25 Jun 2009 18:30:32 +0000
Subject: [PATCH] a couple of additions to the tests, plus a change to the
 artificial resource pool to support the queryContained flag

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1099 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../simpleDataSources/ArtificialResourcePool.java          | 6 +++++-
 .../datasources/simpleDataSources/SAMByIntervalTest.java   | 7 ++++---
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ArtificialResourcePool.java b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ArtificialResourcePool.java
index 452502592..c79b7eab9 100644
--- a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ArtificialResourcePool.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ArtificialResourcePool.java
@@ -68,7 +68,11 @@ public class ArtificialResourcePool extends SAMIteratorPool {
         if (segment instanceof MappedStreamSegment && iterator instanceof ArtificialSAMQueryIterator) {
             ArtificialSAMQueryIterator queryIterator = (ArtificialSAMQueryIterator)iterator;
             MappedStreamSegment mappedSegment = (MappedStreamSegment)segment;
-            queryIterator.queryContained(mappedSegment.locus.getContig(), (int)mappedSegment.locus.getStart(), (int)mappedSegment.locus.getStop());
+            if (!this.queryOverlapping) {
+                queryIterator.queryContained(mappedSegment.locus.getContig(), (int)mappedSegment.locus.getStart(), (int)mappedSegment.locus.getStop());
+            } else {
+                queryIterator.queryOverlapping(mappedSegment.locus.getContig(), (int)mappedSegment.locus.getStart(), (int)mappedSegment.locus.getStop());
+            }
             return queryIterator;
         }
         else if (segment instanceof UnmappedStreamSegment) {
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByIntervalTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByIntervalTest.java
index 520594ae7..ff86c771f 100644
--- a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByIntervalTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByIntervalTest.java
@@ -79,6 +79,7 @@ public class SAMByIntervalTest extends BaseTest {
      */
     @Before
     public void doForEachTest() {
+
         fl = new ArrayList<File>();
 
         // sequence
@@ -122,7 +123,7 @@ public class SAMByIntervalTest extends BaseTest {
      */
     @Test
     public void testSingleRead() {
-        testRead(1,ArtificialSAMUtils.DEFAULT_READ_LENGTH,1);
+        testRead(1,ArtificialSAMUtils.DEFAULT_READ_LENGTH,50);
     }
 
     /**
@@ -130,7 +131,7 @@ public class SAMByIntervalTest extends BaseTest {
      */
     @Test
     public void testChromosome() {
-        testRead(1, READ_COUNT, READ_COUNT -ArtificialSAMUtils.DEFAULT_READ_LENGTH+1); // +1 because we go from 1 up to 101
+        testRead(1, READ_COUNT, READ_COUNT);
     }
 
     /**
@@ -138,7 +139,7 @@ public class SAMByIntervalTest extends BaseTest {
      */
     @Test
     public void testMiddle() {
-        testRead(20, READ_COUNT-20, READ_COUNT -ArtificialSAMUtils.DEFAULT_READ_LENGTH-40+2);
+        testRead(20, READ_COUNT-20,61);
     }