From a5dee8a42eea8760c4499807091e219bf7174ec9 Mon Sep 17 00:00:00 2001
From: Phillip Dexheimer <phildex@broadinstitute.org>
Date: Thu, 4 Dec 2014 23:15:09 -0500
Subject: [PATCH] Fix NPE in SplitSamFile   * PT 82892316   * Added integration
 test   * Fixed similar error in debug output of HC

---
 .../haplotypecaller/HaplotypeCaller.java      |  2 +
 .../tools/walkers/readutils/SplitSamFile.java |  4 ++
 .../SplitSamFileIntegrationTest.java          | 60 +++++++++++++++++++
 3 files changed, 66 insertions(+)
 create mode 100644 public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
index 2f1b4ba3b..5922defb1 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -59,6 +59,7 @@ import htsjdk.variant.vcf.*;
 import org.broadinstitute.gatk.engine.CommandLineGATK;
 import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
 import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
+import org.broadinstitute.gatk.engine.io.DirectOutputTracker;
 import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils;
@@ -1201,6 +1202,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
             // Capture any exception that might be thrown, and write out the assembly failure BAM if requested
             if ( captureAssemblyFailureBAM ) {
                 final SAMFileWriter writer = SAMFileWriterStub.createSAMFileWriter("assemblyFailure.bam", getToolkit());
+                new DirectOutputTracker().addOutput((SAMFileWriterStub) writer);
                 for ( final GATKSAMRecord read : activeRegion.getReads() ) {
                     writer.addAlignment(read);
                 }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java
index 3ef03c3d6..500ce20d2 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java
@@ -30,6 +30,8 @@ import htsjdk.samtools.SAMFileWriter;
 import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.SAMRecord;
 import org.apache.log4j.Logger;
+import org.broadinstitute.gatk.engine.io.DirectOutputTracker;
+import org.broadinstitute.gatk.engine.io.OutputTracker;
 import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub;
 import org.broadinstitute.gatk.utils.commandline.Argument;
 import org.broadinstitute.gatk.engine.CommandLineGATK;
@@ -104,6 +106,7 @@ public class SplitSamFile extends ReadWalker<SAMRecord, Map<String, SAMFileWrite
         }
 
         HashMap<String, SAMFileWriter> outputs = new HashMap<>();
+        final OutputTracker outputTracker = new DirectOutputTracker();
         for ( Map.Entry<String, SAMFileHeader> elt : headers.entrySet() ) {
             final String sample = elt.getKey();
             final String filename = outputRoot + sample + ".bam";
@@ -111,6 +114,7 @@ public class SplitSamFile extends ReadWalker<SAMRecord, Map<String, SAMFileWrite
 
             final SAMFileWriter output = SAMFileWriterStub.createSAMFileWriter(filename, getToolkit(), elt.getValue());
             outputs.put(sample, output);
+            outputTracker.addOutput( (SAMFileWriterStub) output);
         }
 
         return outputs;
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java
new file mode 100644
index 000000000..5a5258b3d
--- /dev/null
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java
@@ -0,0 +1,60 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.readutils;
+
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.Collections;
+
+public class SplitSamFileIntegrationTest extends WalkerTest {
+
+    @Test
+    public void testSplitSamFile() {
+        final String prefix = "splitsam";
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SplitSamFile" +
+                        " -R " + b37KGReference +
+                        " -I " + privateTestDir+"/CEUTrio.HiSeq.b37.MT.1_50.bam" +
+                        " --outputRoot " + prefix,
+                Collections.<String>emptyList()
+        );
+        addSplitOutput(spec, prefix, "NA12878", "b1a57327a3f0bdbe167dbc7d547f1247");
+        addSplitOutput(spec, prefix, "NA12891", "3bb331fd468fc91c548f38857473f399");
+        addSplitOutput(spec, prefix, "NA12892", "ac61ae9cd168ac15e3a03fe7ab51fb22");
+        executeTest("testSplitSamFile", spec);
+    }
+
+    private void addSplitOutput(final WalkerTestSpec spec, final String outputPrefix, final String sample, final String md5) {
+        final File outputFile = new File(outputPrefix + sample + ".bam");
+        spec.addAuxFile(md5, outputFile);
+
+        //The AuxFile mechanism will ensure the bam is deleted, but it doesn't know about indices
+        new File(outputFile.getAbsolutePath() + ".bai").deleteOnExit();
+        new File(outputFile.getAbsolutePath().replaceAll("bam$", ".bai")).deleteOnExit();
+    }
+}