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Merge pull request #1019 from broadinstitute/rhl_var_index_param_gz 

Indexing parameters not required if output file has the g.vcf.gz exte…
This commit is contained in:
Geraldine Van der Auwera 2015-06-17 14:30:20 -04:00
parent a4987310ae b35085ca28
commit 719bb15340
4 changed files with 34 additions and 4 deletions
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5
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -1204,9 +1204,10 @@ 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 extension
* @return true if the VCF output file has a .g.vcf or .g.vcf.gz extension
*/
private boolean isGVCF() {
return ((VariantContextWriterStub) vcfWriter).getOutputFile().getName().endsWith("." + GATKVCFUtils.GVCF_EXT);
String fileName = ((VariantContextWriterStub) vcfWriter).getOutputFile().getName();
return ( fileName.endsWith("." + GATKVCFUtils.GVCF_EXT) || fileName.endsWith("." + GATKVCFUtils.GVCF_GZ_EXT) );
}
}

12
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
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@ -224,6 +224,18 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
executeTest("testGVCFIndexNoThrow", spec);
}
/**
* Test HaplotypeCaller to ensure it does not throw an exception when a .g.vcf.gz output file is specified and the indexing arguments are omitted
*/
@Test()
public void testGVCFGzIndexNoThrow() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000000-17000100");
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(GATKVCFUtils.GVCF_GZ_EXT), Arrays.asList(""));
spec.disableShadowBCF();
executeTest("testGVCFIndexNoThrow", spec);
}
@Test()
public void testWrongParameterGVCFIndexException() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",

5
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java
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@ -69,8 +69,9 @@ public class GATKVCFUtils {
public final static GATKVCFIndexType DEFAULT_GVCF_INDEX_TYPE = GATKVCFIndexType.LINEAR;
public final static Integer DEFAULT_GVCF_INDEX_PARAMETER = 128000;
// GVCF file extension
// GVCF file extensions
public final static String GVCF_EXT = "g.vcf";
public final static String GVCF_GZ_EXT = "g.vcf.gz";
// Message for using the deprecated --variant_index_type or --variant_index_parameter arguments.
public final static String DEPRECATED_INDEX_ARGS_MSG = "Naming your output file using the .g.vcf extension will automatically set the appropriate values " +
@ -389,7 +390,7 @@ public class GATKVCFUtils {
indexType = variantIndexType;
indexParameter = variantIndexParameter;
logger.warn(DEPRECATED_INDEX_ARGS_MSG);
} else if (outputFile.getName().endsWith("." + GVCF_EXT)) {
} else if (outputFile.getName().endsWith("." + GVCF_EXT) || outputFile.getName().endsWith("." + GVCF_GZ_EXT)) {
indexType = DEFAULT_GVCF_INDEX_TYPE;
indexParameter = DEFAULT_GVCF_INDEX_PARAMETER;
}

16
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
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@ -246,4 +246,20 @@ public class CatVariantsIntegrationTest {
ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cmdLine));
pc.execAndCheck(ps);
}
@Test()
public void testCatVariantsGVCFGzIndexCreation() throws IOException{
String cmdLine = String.format("java -cp \"%s\" %s -R %s -V %s -V %s -out %s",
StringUtils.join(RuntimeUtils.getAbsoluteClassPaths(), File.pathSeparatorChar),
CatVariants.class.getCanonicalName(),
BaseTest.b37KGReference,
CatVariantsVcf1,
CatVariantsVcf2,
BaseTest.createTempFile("CatVariantsGVCFIndexCreationTest", "." + GATKVCFUtils.GVCF_GZ_EXT));
ProcessController pc = ProcessController.getThreadLocal();
ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cmdLine));
pc.execAndCheck(ps);
}
}