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I think the VR integration tests are fine. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4240 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2010-09-09 15:00:41 +00:00
parent 6a30617a60
commit d625186796
1 changed files with 26 additions and 27 deletions
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53
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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@ -11,35 +11,34 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
static HashMap<String, String> tranchesFiles = new HashMap<String, String>();
static HashMap<String, String> inputVCFFiles = new HashMap<String, String>();
// commented out until fixed in SVN
// @Test
// public void testGenerateVariantClusters() {
// HashMap<String, String> e = new HashMap<String, String>();
// e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "7c5431a560e9ca257523cf68b808b058" );
// e.put( validationDataLocation + "lowpass.N3.chr1.raw.vcf", "a438635bc96a80c5e6f090d82a394819" );
@Test
public void testGenerateVariantClusters() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "7c5431a560e9ca257523cf68b808b058" );
e.put( validationDataLocation + "lowpass.N3.chr1.raw.vcf", "a438635bc96a80c5e6f090d82a394819" );
// for ( Map.Entry<String, String> entry : e.entrySet() ) {
// String vcf = entry.getKey();
// String md5 = entry.getValue();
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String vcf = entry.getKey();
String md5 = entry.getValue();
// WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
// "-R " + b36KGReference +
// " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
// " -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/genotypes_r27_nr.b36_fwd.vcf" +
// " -weightDBSNP 0.2 -weightHapMap 1.0" +
// " -T GenerateVariantClusters" +
// " -B:input,VCF " + vcf +
// " -L 1:50,000,000-200,000,000" +
// " -qual 50.0" +
// " --ignore_filter GATK_STANDARD" +
// " -an QD -an HRun -an SB" +
// " -clusterFile %s",
// 1, // just one output file
// Arrays.asList(md5));
// List<File> result = executeTest("testGenerateVariantClusters", spec).getFirst();
// clusterFiles.put(vcf, result.get(0).getAbsolutePath());
// }
// }
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/genotypes_r27_nr.b36_fwd.vcf" +
" -weightDBSNP 0.2 -weightHapMap 1.0" +
" -T GenerateVariantClusters" +
" -B:input,VCF " + vcf +
" -L 1:50,000,000-200,000,000" +
" -qual 50.0" +
" --ignore_filter GATK_STANDARD" +
" -an QD -an HRun -an SB" +
" -clusterFile %s",
1, // just one output file
Arrays.asList(md5));
List<File> result = executeTest("testGenerateVariantClusters", spec).getFirst();
clusterFiles.put(vcf, result.get(0).getAbsolutePath());
}
}
@Test
public void testVariantRecalibrator() {