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Added unit tests for header repairing capabilities in the GATK engine

This commit is contained in:
Mark DePristo 2012-07-01 15:38:10 -04:00
parent 480b32e759
commit 7aff4446d4
2 changed files with 36 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
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@ -564,6 +564,6 @@ class VCFWriter extends IndexingVariantContextWriter {
+ " at " + vc.getChr() + ":" + vc.getStart()
+ " but this key isn't defined in the VCFHeader. The GATK now requires all VCFs to have"
+ " complete VCF headers by default. This error can be disabled with the engine argument"
+ " -U LENIENT_VCF_PROCESSING");
+ " -U LENIENT_VCF_PROCESSING or repair the VCF file header using repairVCFHeader");
}
}

35
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.utils.codecs.vcf;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;
import java.io.File;
@ -66,4 +67,38 @@ public class VCFIntegrationTest extends WalkerTest {
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("63a2e0484ae37b0680514f53e0bf0c94"));
executeTest("Test reading samtools WEx BCF example", spec1);
}
//
//
// Tests to ensure that -U LENIENT_VCF_PROCESS and header repairs are working
//
//
@Test
public void testFailingOnVCFWithoutHeaders() {
runVCFWithoutHeaders("", "", UserException.class, false);
}
@Test
public void testPassingOnVCFWithoutHeadersWithLenientProcessing() {
runVCFWithoutHeaders("-U LENIENT_VCF_PROCESSING", "6de8cb7457154dd355aa55befb943f88", null, true);
}
@Test
public void testPassingOnVCFWithoutHeadersRepairingHeaders() {
runVCFWithoutHeaders("-repairVCFHeader " + privateTestDir + "vcfexample2.justHeader.vcf", "ff61e9cad6653c7f93d82d391f7ecdcb", null, false);
}
private void runVCFWithoutHeaders(final String moreArgs, final String expectedMD5, final Class expectedException, final boolean disableBCF) {
final String testVCF = privateTestDir + "vcfexample2.noHeader.vcf";
final String baseCommand = "-R " + b37KGReference
+ " --no_cmdline_in_header -o %s "
+ "-T VariantsToVCF -V " + testVCF + " " + moreArgs;
WalkerTestSpec spec1 = expectedException != null
? new WalkerTestSpec(baseCommand, 1, expectedException)
: new WalkerTestSpec(baseCommand, 1, Arrays.asList(expectedMD5));
if ( disableBCF )
spec1.disableShadowBCF();
executeTest("Test reading VCF without header lines with additional args " + moreArgs, spec1);
}
}