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Fixed yet another NPE related to the ArgumentTypeDescriptor vs. ArgumentMatchValue. Added integration test based on GSA-621.

This commit is contained in:
Khalid Shakir 2012-10-22 12:04:23 -04:00
parent ccae6a5b92
commit 97dc3664c9
2 changed files with 11 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
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@ -151,7 +151,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
? new VariantContextWriterStub(engine, writerFile, argumentSources) ? new VariantContextWriterStub(engine, writerFile, argumentSources)
: new VariantContextWriterStub(engine, defaultOutputStream, argumentSources); : new VariantContextWriterStub(engine, defaultOutputStream, argumentSources);
stub.setCompressed(isCompressed(writerFileName.asString())); stub.setCompressed(isCompressed(writerFileName == null ? null: writerFileName.asString()));
stub.setDoNotWriteGenotypes(argumentIsPresent(createSitesOnlyArgumentDefinition(),matches)); stub.setDoNotWriteGenotypes(argumentIsPresent(createSitesOnlyArgumentDefinition(),matches));
stub.setSkipWritingCommandLineHeader(argumentIsPresent(createNoCommandLineHeaderArgumentDefinition(),matches)); stub.setSkipWritingCommandLineHeader(argumentIsPresent(createNoCommandLineHeaderArgumentDefinition(),matches));
stub.setForceBCF(argumentIsPresent(createBCFArgumentDefinition(),matches)); stub.setForceBCF(argumentIsPresent(createBCFArgumentDefinition(),matches));

10
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -7,6 +7,7 @@ import org.testng.annotations.Test;
import java.io.File; import java.io.File;
import java.util.Arrays; import java.util.Arrays;
import java.util.Collections;
import java.util.List; import java.util.List;
// ********************************************************************************** // // ********************************************************************************** //
@ -18,6 +19,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129; private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129; private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132; private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132;
private final static String baseCommandNoCmdLineHeaderStdout = "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam";
// -------------------------------------------------------------------------------------------------------------- // --------------------------------------------------------------------------------------------------------------
// //
@ -175,6 +177,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest("test using comp track", spec); executeTest("test using comp track", spec);
} }
@Test
public void testNoCmdLineHeaderStdout() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandNoCmdLineHeaderStdout + " -glm INDEL -L 1:67,225,396-67,288,518", 0,
Collections.<String>emptyList());
executeTest("testNoCmdLineHeaderStdout", spec);
}
@Test @Test
public void testOutputParameterSitesOnly() { public void testOutputParameterSitesOnly() {
testOutputParameters("-sites_only", "97ba874eafc9884a4de027a84c036311"); testOutputParameters("-sites_only", "97ba874eafc9884a4de027a84c036311");