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Fixing integration tests I broke yesterday; removing batch merging test since we don't support that anymore.

This commit is contained in:
Eric Banks 2011-07-13 10:01:23 -04:00
parent 6007eea3ff
commit 797c50e689
3 changed files with 6 additions and 52 deletions
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6
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
View File

@ -23,7 +23,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
+ " -L chr20:556259-756570",
1,
Arrays.asList("e312b7d3854d5b2834a370659514a813"));
Arrays.asList("7f11f7f75d1526077f0173c7ed1fc6c4"));
executeTest("Merge MNP sites within genomic distance of 1 [TEST ONE]", spec);
}
@ -33,7 +33,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
+ " -L chr20:556259-756570",
1,
Arrays.asList("681f50e45f1d697370d2c355df2e18bc"));
Arrays.asList("53dd312468296826bdd3c22387390c88"));
executeTest("Merge MNP sites within genomic distance of 10 [TEST TWO]", spec);
}
@ -43,7 +43,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
+ " -L chr20:556259-756570",
1,
Arrays.asList("0bccb0ef928a108418246bec01098083"));
Arrays.asList("e26f92d2fb9f4eaeac7f9d8ee27410ee"));
executeTest("Merge MNP sites within genomic distance of 100 [TEST THREE]", spec);
}

6
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java
View File

@ -23,7 +23,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
+ " -L chr20:556259-756570",
1,
Arrays.asList("e16f957d888054ae0518e25660295241"));
Arrays.asList("af5e1370822551c0c6f50f23447dc627"));
executeTest("Merge sites within genomic distance of 1 [TEST ONE]", spec);
}
@ -33,7 +33,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
+ " -L chr20:556259-756570",
1,
Arrays.asList("122a482090677c7619c2105d44e00d11"));
Arrays.asList("dd8c44ae1ef059a7fe85399467e102eb"));
executeTest("Merge sites within genomic distance of 10 [TEST TWO]", spec);
}
@ -43,7 +43,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
+ " -L chr20:556259-756570",
1,
Arrays.asList("bc6a8c8a42bb2601db98e88e9ad74748"));
Arrays.asList("f81fd72ecaa57b3215406fcea860bcc5"));
executeTest("Merge sites within genomic distance of 100 [TEST THREE]", spec);
}

46
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java
View File

@ -1,46 +0,0 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import java.io.File;
import java.util.Arrays;
public class BatchMergeIntegrationTest extends WalkerTest {
@Test
public void testBatchMerge1() {
String bam = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
String alleles = validationDataLocation + "batch.merge.alleles.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T UnifiedGenotyper -NO_HEADER -BTI alleles -stand_call_conf 0.0 -glm BOTH -G none -nsl -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -o %s -R " + b37KGReference
+ " -B:alleles,VCF " + alleles
+ " -I " + bam,
1,
Arrays.asList("f4ed8f4ef2cba96823c06e90e9d0de35"));
executeTest("testBatchMerge UG genotype given alleles:" + new File(bam).getName() + " with " + new File(alleles).getName(), spec);
}
}