zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge pull request #783 from broadinstitute/pd_splitsamfile 

Fix NPE in SplitSamFile
This commit is contained in:
rpoplin 2014-12-08 09:39:03 -05:00
parent 5f2a2642d6 a5dee8a42e
commit bf2911d62c
3 changed files with 66 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -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);
}

4
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java
View File

@ -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;

60
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java 100644
View File

@ -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();
}
}