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Disable shadowBCF for VariantRecalibrationWalkers tests because it cannot handle symbolic alleles yet

This commit is contained in:
Mark DePristo 2012-06-22 13:05:59 -04:00
parent 61f0c46423
commit 7b96263f8b
2 changed files with 3 additions and 1 deletions
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2
public/java/test/org/broadinstitute/sting/WalkerTest.java
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@ -79,7 +79,7 @@ public class WalkerTest extends BaseTest {
public void validateOutputBCFIfPossible(final String name, final File resultFile) { public void validateOutputBCFIfPossible(final String name, final File resultFile) {
final File bcfFile = BCF2Utils.shadowBCF(resultFile); final File bcfFile = BCF2Utils.shadowBCF(resultFile);
if ( bcfFile.exists() ) { if ( bcfFile != null && bcfFile.exists() ) {
logger.warn("Checking shadow BCF output file " + bcfFile + " against VCF file " + resultFile); logger.warn("Checking shadow BCF output file " + bcfFile + " against VCF file " + resultFile);
try { try {
VariantContextTestProvider.assertVCFandBCFFilesAreTheSame(resultFile, bcfFile); VariantContextTestProvider.assertVCFandBCFFilesAreTheSame(resultFile, bcfFile);

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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@ -54,6 +54,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -recalFile %s" + " -recalFile %s" +
" -tranchesFile %s", " -tranchesFile %s",
Arrays.asList(params.recalMD5, params.tranchesMD5)); Arrays.asList(params.recalMD5, params.tranchesMD5));
spec.disableShadowBCF(); // TODO -- enable when we support symbolic alleles
executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst(); executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst();
} }
@ -101,6 +102,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -recalFile %s" + " -recalFile %s" +
" -tranchesFile %s", " -tranchesFile %s",
Arrays.asList(params.recalMD5, params.tranchesMD5)); Arrays.asList(params.recalMD5, params.tranchesMD5));
spec.disableShadowBCF(); // TODO -- enable when we support symbolic alleles
executeTest("testVariantRecalibratorIndel-"+params.inVCF, spec).getFirst(); executeTest("testVariantRecalibratorIndel-"+params.inVCF, spec).getFirst();
} }