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Finishing previous checkin 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3608 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-22 17:21:38 +00:00
parent 4727bcda24
commit 824c2bbac0
2 changed files with 1 additions and 21 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
View File

@ -81,7 +81,7 @@ public class TrioGenotyperWalker extends RefWalker<VariantContext, Integer>{
private VCFWriter writer = null;
public void initialize() {
UGEngine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, null, null);
UGEngine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, null);
// initialize the header
FAMILY_MEMBERS = Arrays.asList(mom, dad, kid);

20
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -112,26 +112,6 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest("testConfidence2", spec2);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing beagle output
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testOtherOutput() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper" +
" -R " + oneKGLocation + "reference/human_b36_both.fasta" +
" -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam" +
" -varout /dev/null" +
" -beagle %s" +
" -L 1:10,023,400-10,024,000",
1,
Arrays.asList("0a6f06f1900c2b965a1d0ac413df8151"));
executeTest(String.format("testOtherOutput"), spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing other output formats