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Update to MD5s for old tests and added extensive VCF testing 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2615 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-01-16 20:22:58 +00:00
parent 64225b28fd
commit d8e74c5795
1 changed files with 29 additions and 1 deletions
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30
java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
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@ -19,7 +19,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
public void testEvalVariantROD() {
HashMap<String, String> md5 = new HashMap<String, String>();
md5.put("", "d6b8c2d6c37d42d1ca2288799a8bd8e4");
md5.put("-A", "b868aac194f6d0bd1fd2c0c63ddfaeab");
md5.put("-A", "0294b2e3915e88dfe2547e9db64ed1b3");
/**
* the above MD5 was calculated from running the following command:
@ -189,5 +189,33 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
md5);
List<File> result = executeTest("testEvalRuntimeWithLotsOfIntervals", spec).getFirst();
}
@Test
public void testVCFVariantEvals() {
HashMap<String, String> md5 = new HashMap<String, String>();
md5.put("", "3dda57ac7a9c8f3800726c9affb9d9bd");
md5.put("-A", "d985e61fd0d7fc34c9c1a553e2881c67");
md5.put("-A --includeFilteredRecords", "434c60986aa54c5fd07c22df1910ec44");
md5.put("-A --sampleName NA12878", "aff844b88f71824a6cd3cce553325b17");
md5.put("-A -vcfInfoSelector AF=0.50", "9ab9fa5d89cd6e3278d0d2b13cabbd51");
for ( Map.Entry<String, String> e : md5.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + oneKGLocation + "reference/human_b36_both.fasta" +
" --rodBind eval,VCF," + validationDataLocation + "NA12878.example1.vcf" +
" -T VariantEval" +
" --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
" -hc /humgen/gsa-scr1/GATK_Data/1KG_gffs/NA12878.1kg.gff" +
" -G" +
" -L 1:1-10,000" +
" --outerr %s" +
" --supressDateInformation " + e.getKey(),
1, // just one output file
Arrays.asList(e.getValue()));
List<File> result = executeTest("testVCFVariantEvals", spec).getFirst();
}
}
}