From 4a33cdacde638d28a2baedb9a0caadae878587d1 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 26 Jan 2011 23:48:04 +0000
Subject: [PATCH] Some basic integration tests detecting breakage in OTF BAM
 index generation. Doing it manually for the moment so that there's at least
 something testing this capability; will followup eventually with Mark to see
 whether we can shape the VCF index generation code in such a way that it
 supports BAM index testing as well.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5093 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/WalkerTest.java  |  7 +++++
 .../DepthOfCoverageIntegrationTest.java       |  6 ----
 .../interval/IntervalIntegrationTest.java     | 31 +++++++++++++------
 3 files changed, 28 insertions(+), 16 deletions(-)

diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java
index 70307230f..eebddae1d 100755
--- a/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -247,4 +247,11 @@ public class WalkerTest extends BaseTest {
             }
         }
     }
+
+
+    protected File createTempFileFromBase(String name) {
+        File fl = new File(name);
+        fl.deleteOnExit();
+        return fl;
+    }    
 }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
index 69281fdad..74c990c44 100644
--- a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
@@ -94,10 +94,4 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
 
         execute("testNoCoverageDueToFiltering",spec);
     }
-
-    public File createTempFileFromBase(String name) {
-        File fl = new File(name);
-        fl.deleteOnExit();
-        return fl;
-    }
 }
diff --git a/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java b/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
index 638710ad4..1013417cc 100644
--- a/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.utils.interval;
 import org.broadinstitute.sting.WalkerTest;
 import org.testng.annotations.Test;
 
+import java.io.File;
 import java.util.Arrays;
 import java.util.Collections;
 
@@ -63,31 +64,41 @@ public class IntervalIntegrationTest extends WalkerTest {
 
     @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));
+                        " -U --index_output_bam_on_the_fly",
+                        0, // two output files
+                        Collections.<String>emptyList());
+
+        // our base file
+        File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
+        this.setOutputFileLocation(baseOutputFile);
+        spec.addAuxFile("fcd11cfa8474472c617d400623a30fcd",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("3d1f077727e6b68e20a2095d034e56d7", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
+
         executeTest("testUnmappedReadInclusion",spec);
     }
 
     @Test(enabled = true)
     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));
+                        " -U --index_output_bam_on_the_fly",
+                        0, // two output files
+                        Collections.<String>emptyList());
+
+        // our base file
+        File baseOutputFile = createTempFile("testUnmappedReadExclusion",".bam");
+        this.setOutputFileLocation(baseOutputFile);
+        spec.addAuxFile("3153593c9f9ff80a8551fff5655e65ec",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("7fc574ac72211623e4df74d9f75a4e48", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
+
         executeTest("testUnmappedReadExclusion",spec);
     }