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Merge pull request #1265 from broadinstitute/rhl_hc_stdout_1259 

Fix exception when writing gVCF to stdout
This commit is contained in:
Ron Levine 2015-12-29 23:07:53 -05:00
parent 7089824e1b aa5e88a393
commit 4b3b5636c6
2 changed files with 18 additions and 3 deletions
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12
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -104,6 +104,7 @@ import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import org.broadinstitute.gatk.utils.sam.ReadUtils;
import org.broadinstitute.gatk.utils.variant.*;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.*;
@ -1245,10 +1246,15 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
/**
* Is writing to an output GVCF file?
*
* @return true if the VCF output file has a .g.vcf or .g.vcf.gz extension
* @return true if the VCF output file has a .g.vcf or .g.vcf.gz extension or if no output file
*/
private boolean isGVCF() {
String fileName = ((VariantContextWriterStub) vcfWriter).getOutputFile().getName();
return ( fileName.endsWith("." + GATKVCFUtils.GVCF_EXT) || fileName.endsWith("." + GATKVCFUtils.GVCF_GZ_EXT) );
final File file = ((VariantContextWriterStub) vcfWriter).getOutputFile();
if ( file == null ){
return true;
} else {
final String fileName = file.getName();
return ( fileName.endsWith("." + GATKVCFUtils.GVCF_EXT) || fileName.endsWith("." + GATKVCFUtils.GVCF_GZ_EXT) );
}
}
}

9
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -368,6 +368,15 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
executeTest("testGraphBasedNoSuchEdgeBugFix", spec);
}
@Test
public void testWriteGVCFStdout() {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -dontTrimActiveRegions -ERC GVCF ",
b37KGReferenceWithDecoy, privateTestDir + "graphbased_no_such_edge_bug.bam", privateTestDir + "graphbased_no_such_edge_bug.intervals.bed");
final WalkerTestSpec spec = new WalkerTestSpec(commandLine, Arrays.asList(""));
spec.disableShadowBCF();
executeTest("testWriteGVCFStdout", spec);
}
// This test takes longer than 15 secs ... ~ 25-35 ,
@Test
public void testLackSensitivityDueToBadHaplotypeSelectionFix() {