From acfe83920b8a84f5bc1b596a1b1f85a87ed78213 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 15 Dec 2010 23:11:46 +0000
Subject: [PATCH] '-L unmapped': adding integration tests for explicitly
 including (-L unmapped) unmapped reads and explicitly excluding (-XL
 unmapped) unmapped reads, augmenting the suite of unit tests already put in
 place.

'-L unmapped' seems safe to use; go for it, but please validate results against
samtools flagstat when the process finishes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4849 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../interval/IntervalIntegrationTest.java     | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java b/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
index bf085e69e..98df83254 100644
--- a/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
@@ -60,4 +60,36 @@ public class IntervalIntegrationTest extends WalkerTest {
                         Arrays.asList(md5));                        
         executeTest("testAllIntervalsExplicit",spec);
     }
+
+    @Test
+    public void testUnmappedReadInclusion() {
+        String md5 = "fcd11cfa8474472c617d400623a30fcd";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T PrintReads" +
+                        " -I " + validationDataLocation + "MV1994.bam" +
+                        " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
+                        " -L unmapped" +
+                        " -o %s" +
+                        " -U",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testUnmappedReadInclusion",spec);
+    }
+
+    @Test
+    public void testUnmappedReadExclusion() {
+        String md5 = "3153593c9f9ff80a8551fff5655e65ec";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T PrintReads" +
+                        " -I " + validationDataLocation + "MV1994.bam" +
+                        " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
+                        " -XL unmapped" +
+                        " -o %s" +
+                        " -U",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testUnmappedReadExclusion",spec);
+    }
+
+
 }