From 70b07206a243d54d7cf13152287256b607ee2b6f Mon Sep 17 00:00:00 2001 From: depristo Date: Mon, 19 Jul 2010 22:41:48 +0000 Subject: [PATCH] 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 --- .../CombineVariantsIntegrationTest.java | 27 +++++++++---------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index 5de98bd0f..56584012e 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -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", ""); } }