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CombineVariants tests for Guillermo and Eric to explore the correctness of the in/out reader, writer behavior of the system. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3834 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-07-19 22:41:48 +00:00
parent c47a5ff5ab
commit 70b07206a2
1 changed files with 13 additions and 14 deletions
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27
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
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@ -39,33 +39,32 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
return "-T CombineVariants -L 1:1-50,000,000 -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta" + args;
}
// todo -- merge with one file should be identical to input
public void test1InOut(String file, String type, String md5) {
public void test1InOut(String file, String md5) {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -priority v1 -B v1," + type + "," + validationDataLocation + file),
baseTestString(" -priority v1 -B v1,VCF," + validationDataLocation + file),
1,
Arrays.asList(md5));
executeTest("testInOut1--" + file, spec);
}
public void combine2(String file1, String type1, String file2, String type2, String md5) {
public void combine2(String file1, String file2, String md5) {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -priority v1,v2 -B v1," + type1 + "," + validationDataLocation + file1 + " -B v2," + type2 + "," + validationDataLocation + file2),
baseTestString(" -priority v1,v2 -B v1,VCF," + validationDataLocation + file1 + " -B v2,VCF," + validationDataLocation + file2),
1,
Arrays.asList(md5));
executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
}
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "VCF", ""); }
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "VCF4", ""); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "VCF4", ""); }
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", ""); }
@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", ""); } // official project VCF files in tabix format
@Test public void combineSNPsAndIndels() { combine2("pilot2.snps.vcf4.genotypes.vcf", "VCF", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "VCF4", ""); }
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "VCF4", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "VCF4", ""); }
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", ""); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", ""); }
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "VCF", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "VCF", ""); }
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "2ec9e7acff0c36c2b51b2b720944bcde"); } // official project VCF files in tabix format
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", ""); }
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", ""); }
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", ""); }
}