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Disabling bcf2 reading from samtools because it's 1 basis; updating select variants integrationtest

This commit is contained in:
Mark DePristo 2012-07-02 15:55:42 -04:00
parent 602729c09d
commit 1b0a775773
2 changed files with 2 additions and 2 deletions
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2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
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@ -64,7 +64,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile), baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
1, 1,
Arrays.asList("433eccaf1ac6e6be500ef0984a5d8d8b") Arrays.asList("4386fbb258dcef4437495a37f5a83c53")
); );
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest("testComplexSelection--" + testfile, spec); executeTest("testComplexSelection--" + testfile, spec);

2
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
View File

@ -59,7 +59,7 @@ public class VCFIntegrationTest extends WalkerTest {
executeTest("Test writing samtools WEx BCF example", spec1); executeTest("Test writing samtools WEx BCF example", spec1);
} }
@Test @Test(enabled = false) // TODO disabled because current BCF2 is 1 based
public void testReadingSamtoolsWExBCFExample() { public void testReadingSamtoolsWExBCFExample() {
String testVCF = privateTestDir + "ex2.bcf"; String testVCF = privateTestDir + "ex2.bcf";
String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s "; String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";