Updating MD5s to latest version to reflect inclusion of contigs in headers
This commit is contained in:
Mark DePristo
parent
0e81484f0f
commit
aa2178cc68
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@ -24,7 +24,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString(b36KGReference, "symbolic_alleles_1.vcf"),
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1,
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Arrays.asList("444a20659f67592a8284e0b7849e4302"));
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Arrays.asList("c79137da24ad4dc15cedc742de39247f"));
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executeTest("Test symbolic alleles", spec);
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}
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@ -33,7 +33,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
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1,
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Arrays.asList("93a24c019663a6011b4d6de12538df11"));
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Arrays.asList("3f6cbbd5fdf164d87081a3af19eeeba7"));
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executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
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}
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}
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@ -16,7 +16,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsNotAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --variant:VCF3 " + testDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("5720826c2bf6cbc762e4a888ef58c3f2"));
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Arrays.asList("dfa5dff09fa964b06da19c0f4aff6928"));
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executeTest("test file has annotations, not asking for annotations, #1", spec);
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}
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@ -24,7 +24,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsNotAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --variant:VCF3 " + testDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("088e5db7d8de6606cd562885fa47f3b2"));
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Arrays.asList("9914bd19f6235c550e5182e0f4591da6"));
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executeTest("test file has annotations, not asking for annotations, #2", spec);
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}
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@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF3 " + testDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("37fd6826db907f80d4631bae1b629da4"));
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Arrays.asList("6a52ef10bb10d72cdd82a8f7afc2dd09"));
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executeTest("test file has annotations, asking for annotations, #1", spec);
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}
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@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF3 " + testDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("8a85c20b219a8bb286df3c9f4e1cdc8c"));
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Arrays.asList("edf35b2cfd033d5abafc33fe739759e2"));
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executeTest("test file has annotations, asking for annotations, #2", spec);
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}
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@ -48,7 +48,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsNotAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --variant:VCF3 " + testDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("da446d3a3e9aefa7537b65b5adc3609b"));
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Arrays.asList("dd89dfa22f0e1d6760095e04f528d62a"));
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executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
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}
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@ -58,7 +58,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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// they don't get reordered. It's a good test of the genotype ordering system.
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --variant:VCF3 " + testDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("04c71d90e3df9d519160636ceb0f02b9"));
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Arrays.asList("542d9ed8290ef7868387af4127e0b5fa"));
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executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
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}
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@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF3 " + testDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("6d64723c808a3dd774ed06e228f9c63d"));
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Arrays.asList("b1b32ed3b831c92c94258c8e4a60e8c9"));
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executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
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}
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@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF3 " + testDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("153a23b2fa4eb0ee288e4bb2f0fc4bf8"));
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Arrays.asList("7e5b8ad0c7005036e39739de77546023"));
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executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
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}
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@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testExcludeAnnotations() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + testDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("a28a503ab204474ecee306c9eceb1060"));
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Arrays.asList("ef046909a6f6c6cb43653a255a99a014"));
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executeTest("test exclude annotations", spec);
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}
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@ -90,7 +90,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testOverwritingHeader() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + testDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
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Arrays.asList("1d98be77dad9c703402de0315db5176a"));
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Arrays.asList("341fbac1802c54b1ee658b4bb54e963e"));
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executeTest("test overwriting header", spec);
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}
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@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoReads() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + testDir + "vcfexample3empty.vcf -L " + testDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("ea6201db7c1fd5cb9cc3110a3396c646"));
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Arrays.asList("f44f1a10a2e3b8e749d1903db7429f44"));
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executeTest("not passing it any reads", spec);
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}
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@ -106,7 +106,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testDBTagWithDbsnp() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + testDir + "vcfexample3empty.vcf -L " + testDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("5103b9d9857530dc0ccdb8ca0a1db8c3"));
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Arrays.asList("cb0ee4261b72caf652c77c6d75bc7c85"));
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executeTest("getting DB tag with dbSNP", spec);
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}
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@ -114,7 +114,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testMultipleIdsWithDbsnp() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + " -G Standard --variant " + testDir + "vcfexample3withIDs.vcf -L " + testDir + "vcfexample3withIDs.vcf", 1,
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Arrays.asList("d519c21ab0ae901d39856fea7e0e9d83"));
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Arrays.asList("e2b9cb00137bb4f2cb86b77d30b35dd3"));
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executeTest("adding multiple IDs with dbSNP", spec);
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}
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@ -122,7 +122,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testDBTagWithHapMap() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --comp:H3 " + testDir + "fakeHM3.vcf -G Standard --variant " + testDir + "vcfexample3empty.vcf -L " + testDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("746f3a431c6491b85dd6fcf75065550f"));
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Arrays.asList("b501a8f92abb1623e71c4593b68e8b31"));
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executeTest("getting DB tag with HM3", spec);
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}
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@ -130,7 +130,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoQuals() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --variant " + testDir + "noQual.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L " + testDir + "noQual.vcf -A QualByDepth", 1,
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Arrays.asList("7ce09a89e72ee95f21313e496311068a"));
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Arrays.asList("4a247f039dfb16ac05b38a0dd5f98da6"));
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executeTest("test file doesn't have QUALs", spec);
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}
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@ -138,7 +138,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testUsingExpression() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --resource:foo " + testDir + "targetAnnotations.vcf -G Standard --variant:VCF3 " + testDir + "vcfexample3empty.vcf -E foo.AF -L " + testDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("accce2796a967d05d756e1b5adecd6d2"));
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Arrays.asList("33926902898f1c9ad871afe54c64e5b5"));
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executeTest("using expression", spec);
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}
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@ -146,13 +146,13 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testUsingExpressionWithID() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --resource:foo " + testDir + "targetAnnotations.vcf -G Standard --variant:VCF3 " + testDir + "vcfexample3empty.vcf -E foo.ID -L " + testDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("9a37502ab929ac3d5a829467f5612853"));
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Arrays.asList("636d9557a04648e639674069004a2315"));
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executeTest("using expression with ID", spec);
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}
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@Test
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public void testTabixAnnotations() {
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final String MD5 = "bb9a148716fc69d706c5be146c1afa00";
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final String MD5 = "5aebcf8f76c649d645708b1262185c80";
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for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -A HomopolymerRun --variant:vcf " + validationDataLocation + file + " -L " + validationDataLocation + "CEU.exon.2010_03.sites.vcf --no_cmdline_in_header", 1,
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@ -168,7 +168,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile " + validationDataLocation +
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"snpEff2.0.5.AFR.unfiltered.vcf -L 1:1-1,500,000 -L 2:232,325,429",
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1,
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Arrays.asList("bef7201d9c79facbecba15d4abcc684b")
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Arrays.asList("0c20cda1cf0b903a287f1807ae5bee02")
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);
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executeTest("Testing SnpEff annotations", spec);
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}
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@ -187,7 +187,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testTDTAnnotation() {
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final String MD5 = "900e9d82ea3127aa06e676cf50b341f6";
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final String MD5 = "240e31b14db09b5ce43c40e21ca52dc2";
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WalkerTestSpec spec = new WalkerTestSpec(
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"-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + testDir + "ug.random50000.subset300bp.chr1.family.vcf" +
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" -L " + testDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + testDir + "ug.random50000.family.ped -o %s", 1,
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@ -198,7 +198,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testChromosomeCountsPed() {
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final String MD5 = "7fe0e9df2d9fb375beb7cf23afdb4c87";
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final String MD5 = "d8ff51b00001e6f1b2cb7347b024c8bf";
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WalkerTestSpec spec = new WalkerTestSpec(
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"-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --variant:vcf " + testDir + "ug.random50000.subset300bp.chr1.family.vcf" +
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" -L " + testDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + testDir + "ug.random50000.family.ped -o %s", 1,
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@ -208,7 +208,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testInbreedingCoeffPed() {
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final String MD5 = "7aaf0033a823bbf9066b43764d8dd660";
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final String MD5 = "e94d589b5691e3ecfd9cc9475a384890";
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WalkerTestSpec spec = new WalkerTestSpec(
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"-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + testDir + "ug.random50000.subset300bp.chr1.family.vcf" +
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" -L " + testDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + testDir + "ug.random50000.family.ped -o %s", 1,
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@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
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"--beagleR2:BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
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"--beagleProbs:BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
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"--beaglePhased:BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
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"-o %s --no_cmdline_in_header", 1, Arrays.asList("7fd0d0c2d1af3b16378339c181e40611"));
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"-o %s --no_cmdline_in_header", 1, Arrays.asList("74db5bb05f08f4c1dd5a7cf844c903b6"));
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executeTest("test BeagleOutputToVCF", spec);
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}
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@ -50,7 +50,7 @@ public class BeagleIntegrationTest extends WalkerTest {
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WalkerTestSpec spec = new WalkerTestSpec(
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"-T ProduceBeagleInput -R " + hg19Reference + " " +
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"--variant:VCF3 " + beagleValidationDataLocation + "inttestbgl.input.vcf " +
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"-o %s", 1, Arrays.asList("a01c704246f3dd1b9c65774007e51e69"));
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"-o %s", 1, Arrays.asList("689773807c87638de3a74564bd6cee2e"));
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executeTest("test BeagleInput", spec);
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}
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@ -60,7 +60,7 @@ public class BeagleIntegrationTest extends WalkerTest {
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"-T ProduceBeagleInput --variant:VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_HSQ_chr22_14-16m.vcf "+
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"--validation:VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_OMNI_chr22_14-16m.vcf "+
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"-L 22:14000000-16000000 -o %s -bvcf %s -bs 0.8 -valp 0.98 -R /humgen/1kg/reference/human_g1k_v37.fasta --no_cmdline_in_header ",2,
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Arrays.asList("660986891b30cdc937e0f2a3a5743faa","e96ddd51da9f4a797b2aa8c20e404166"));
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Arrays.asList("660986891b30cdc937e0f2a3a5743faa","4b6417f892ccfe5c63b8a60cb0ef3740"));
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executeTest("test BeagleInputWithBootstrap",spec);
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}
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@ -72,7 +72,7 @@ public class BeagleIntegrationTest extends WalkerTest {
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"--beagleR2:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
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"--beagleProbs:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
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"--beaglePhased:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
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"-L 20:1-70000 -o %s --no_cmdline_in_header ",1,Arrays.asList("43865f3f0d975ee2c5912b31393842f8"));
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"-L 20:1-70000 -o %s --no_cmdline_in_header ",1,Arrays.asList("22908352f0e476234706922d6bccdc91"));
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executeTest("testBeagleChangesSitesToRef",spec);
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}
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@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
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public void testNoAction() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("5720826c2bf6cbc762e4a888ef58c3f2"));
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Arrays.asList("dfa5dff09fa964b06da19c0f4aff6928"));
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executeTest("test no action", spec);
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}
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@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
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public void testClusteredSnps() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -window 10 --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("d7c2a4b0c1b2b982847508997ba57ebf"));
|
||||
Arrays.asList("4a4596929f9fe983d8868ca142567781"));
|
||||
executeTest("test clustered SNPs", spec);
|
||||
}
|
||||
|
||||
|
|
@ -32,7 +32,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
|
|||
public void testMask1() {
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(
|
||||
baseTestString() + " -maskName foo --mask:VCF3 " + testDir + "vcfexample2.vcf --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("890774962576c407d8a17ed57cf704c1"));
|
||||
Arrays.asList("1719462cd17986c33e59e45b69df0270"));
|
||||
executeTest("test mask all", spec1);
|
||||
}
|
||||
|
||||
|
|
@ -40,7 +40,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
|
|||
public void testMask2() {
|
||||
WalkerTestSpec spec2 = new WalkerTestSpec(
|
||||
baseTestString() + " -maskName foo --mask:VCF " + testDir + "vcfMask.vcf --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("8864573dbf52908501140e6b0afcbc90"));
|
||||
Arrays.asList("db19ff7d90c82cda09fb3c3878100eb5"));
|
||||
executeTest("test mask some", spec2);
|
||||
}
|
||||
|
||||
|
|
@ -48,7 +48,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
|
|||
public void testMask3() {
|
||||
WalkerTestSpec spec3 = new WalkerTestSpec(
|
||||
baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + testDir + "vcfMask.vcf --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("42a1c08763f151073a49e3c7bb68028b"));
|
||||
Arrays.asList("a9e417cba21585c786d4b9930265ea31"));
|
||||
executeTest("test mask extend", spec3);
|
||||
}
|
||||
|
||||
|
|
@ -56,7 +56,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
|
|||
public void testFilter1() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("ef8100c3b7c67d28571cbda771c414c2"));
|
||||
Arrays.asList("4160904b180d1f62a6bf50de6728ce00"));
|
||||
executeTest("test filter #1", spec);
|
||||
}
|
||||
|
||||
|
|
@ -64,7 +64,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
|
|||
public void testFilter2() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("318ed3874fd42b7da8c59554a25a1fab"));
|
||||
Arrays.asList("df80db30c7836731ac7c8c3d4fc005b4"));
|
||||
executeTest("test filter #2", spec);
|
||||
}
|
||||
|
||||
|
|
@ -72,7 +72,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
|
|||
public void testFilterWithSeparateNames() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("9cb398e78a38a7bc5e839e28c8dae2eb"));
|
||||
Arrays.asList("71ce6c0952831cb68f575aa0173dce2b"));
|
||||
executeTest("test filter with separate names #2", spec);
|
||||
}
|
||||
|
||||
|
|
@ -80,7 +80,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
|
|||
public void testGenotypeFilters1() {
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(
|
||||
baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("b38709f932b969e4267603333863269e"));
|
||||
Arrays.asList("179f7f2a90c0e6c656109aac9b775476"));
|
||||
executeTest("test genotype filter #1", spec1);
|
||||
}
|
||||
|
||||
|
|
@ -88,7 +88,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
|
|||
public void testGenotypeFilters2() {
|
||||
WalkerTestSpec spec2 = new WalkerTestSpec(
|
||||
baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("0e1457e678326e44e92ee13e84414e0f"));
|
||||
Arrays.asList("22e07c27feb9017a130dfb045c5b29b9"));
|
||||
executeTest("test genotype filter #2", spec2);
|
||||
}
|
||||
|
||||
|
|
@ -96,7 +96,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
|
|||
public void testDeletions() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo --variant:VCF " + testDir + "twoDeletions.vcf", 1,
|
||||
Arrays.asList("569546fd798afa0e65c5b61b440d07ac"));
|
||||
Arrays.asList("637256ee5348c1c57f1dadf581b06ed9"));
|
||||
executeTest("test deletions", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -29,7 +29,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
2,
|
||||
Arrays.asList("d54a142d68dca54e478c13f9a0e4c95c","1a37fcc93a73429f9065b942ab771233")
|
||||
Arrays.asList("d54a142d68dca54e478c13f9a0e4c95c","313cc749c7ee97713e4551de39e01ac5")
|
||||
);
|
||||
executeTest("testTrueNegativeMV", spec);
|
||||
}
|
||||
|
|
@ -48,7 +48,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
2,
|
||||
Arrays.asList("883ea7fd2b200c4b7fa95a4f7aa15931","7b1f5309c3d4f4aa7e9061f288dceb68")
|
||||
Arrays.asList("883ea7fd2b200c4b7fa95a4f7aa15931","dd90dad9fd11e1b16e6660c3ca0553e7")
|
||||
);
|
||||
executeTest("testTruePositiveMV", spec);
|
||||
}
|
||||
|
|
@ -67,7 +67,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
2,
|
||||
Arrays.asList("e812d62a3449b74b6948ee7deb8a0790","d00922496759e84c66a4b5e222e36997")
|
||||
Arrays.asList("e812d62a3449b74b6948ee7deb8a0790","b35a86d2cad17f0db7b5e84ddc0e5545")
|
||||
);
|
||||
executeTest("testFalsePositiveMV", spec);
|
||||
}
|
||||
|
|
@ -86,7 +86,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
2,
|
||||
Arrays.asList("e3c572f933a40e1878a2cfa52049517a","0de6cccfec929caa07cd0eeafacbfffd")
|
||||
Arrays.asList("e3c572f933a40e1878a2cfa52049517a","c53b5fd377bef48e9c6035a94db398db")
|
||||
);
|
||||
executeTest("testSpecialCases", spec);
|
||||
}
|
||||
|
|
@ -108,7 +108,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
2,
|
||||
Arrays.asList("b42af3b73a2cb38cfc92f8047dd686b3","a69c3f9c005e852b44c29ab25e87ba0d")
|
||||
Arrays.asList("b42af3b73a2cb38cfc92f8047dd686b3","6f596470740e1a57679bbb38c0126364")
|
||||
);
|
||||
executeTest("testPriorOption", spec);
|
||||
}
|
||||
|
|
@ -128,7 +128,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("d00922496759e84c66a4b5e222e36997")
|
||||
Arrays.asList("b35a86d2cad17f0db7b5e84ddc0e5545")
|
||||
);
|
||||
executeTest("testMVFileOption", spec);
|
||||
}
|
||||
|
|
@ -149,7 +149,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
|
|||
"-fatherAlleleFirst"
|
||||
),
|
||||
2,
|
||||
Arrays.asList("c158a3816357597543ef85c4478c41e8","4f8daca19c8f31bd87850c124f91e330")
|
||||
Arrays.asList("c158a3816357597543ef85c4478c41e8","6d550784382aa910f78b533d889c91c0")
|
||||
);
|
||||
executeTest("testFatherAlleleFirst", spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
|
|||
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
|
||||
+ " -L chr20:332341-382503",
|
||||
1,
|
||||
Arrays.asList("2520f93505fda28d44f618a0123d593b"));
|
||||
Arrays.asList("d78f694499d917b13f0d3e797f04353a"));
|
||||
executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
|
||||
}
|
||||
|
||||
|
|
@ -36,7 +36,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
|
|||
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
|
||||
+ " -L chr20:1232503-1332503",
|
||||
1,
|
||||
Arrays.asList("965b8f448365b7f4a124d32e809eb048"));
|
||||
Arrays.asList("9d9c3cb8b323c3d73af7fc96bc163619"));
|
||||
executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
|
||||
}
|
||||
|
||||
|
|
@ -46,7 +46,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
|
|||
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 2, 30)
|
||||
+ " -L chr20:332341-382503",
|
||||
1,
|
||||
Arrays.asList("60f5bb699335f47cdc505322c5be3803"));
|
||||
Arrays.asList("321f815590992cb52da7a4989c3f2f4c"));
|
||||
executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
|
||||
}
|
||||
|
||||
|
|
@ -56,7 +56,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
|
|||
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 5, 100)
|
||||
+ " -L chr20:332341-382503",
|
||||
1,
|
||||
Arrays.asList("023c2fb43b50807cfd46841ed6f0d215"));
|
||||
Arrays.asList("318f93ca4678a0b246a9f229252ff31d"));
|
||||
executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
|
||||
}
|
||||
|
||||
|
|
@ -66,7 +66,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
|
|||
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 1000, 7, 10)
|
||||
+ " -L chr20:332341-482503",
|
||||
1,
|
||||
Arrays.asList("e5e6e9f84d108d5b001aa53017d2801e"));
|
||||
Arrays.asList("ed5552077aa123814022485ed555b6e0"));
|
||||
executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
|
||||
}
|
||||
|
||||
|
|
@ -76,7 +76,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
|
|||
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
|
||||
+ " -L chr20:652810-681757",
|
||||
1,
|
||||
Arrays.asList("8fc53bfbea2754ff8577460786a3400c"));
|
||||
Arrays.asList("5223d1395d373d2a968d6dd22741ad6c"));
|
||||
executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
|
||||
}
|
||||
|
||||
|
|
@ -86,7 +86,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
|
|||
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "CEU.trio.2010_03.genotypes.hg18.vcf", 20000, 10, 10)
|
||||
+ " -L chr20:332341-802503",
|
||||
1,
|
||||
Arrays.asList("c37548b333b65f58d0edfc5c2a62a28a"));
|
||||
Arrays.asList("44eb225ab3167651ec0a9e1fdcc83d34"));
|
||||
executeTest("Use trio-phased VCF, but ignore its phasing [TEST SEVEN]", spec);
|
||||
}
|
||||
|
||||
|
|
@ -96,7 +96,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
|
|||
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "CEU.trio.2010_03.genotypes.hg18.vcf", 20000, 10, 10)
|
||||
+ " -L chr20:332341-802503" + " -respectPhaseInInput",
|
||||
1,
|
||||
Arrays.asList("dfc7cdddd702e63d46d04f61a3ecd720"));
|
||||
Arrays.asList("e3549b89d49092e73cc6eb21f233471c"));
|
||||
executeTest("Use trio-phased VCF, and respect its phasing [TEST EIGHT]", spec);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(sampleNone + freqUnif + "--variant " + testfile),
|
||||
1,
|
||||
Arrays.asList("6a9e990a9252840904b5144213915b32")
|
||||
Arrays.asList("b8a988757ac1f206d123140da5a3e778")
|
||||
);
|
||||
|
||||
executeTest("testNoSampleSelectionFreqUniform--" + testfile, spec);
|
||||
|
|
@ -45,7 +45,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(sampleNone + freqAF + "--variant " + testfile),
|
||||
1,
|
||||
Arrays.asList("eaa2385086cddff68cf4fdb81cbdbbb9")
|
||||
Arrays.asList("542d5d5ff8c64da7b077bab4b950a9a3")
|
||||
);
|
||||
|
||||
executeTest("testNoSampleSelectionFreqAF--" + testfile, spec);
|
||||
|
|
@ -57,7 +57,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(sampleGT + freqUnif + "--variant " + testfile),
|
||||
1,
|
||||
Arrays.asList("24077656f590d6905546f7e019c8dccb")
|
||||
Arrays.asList("7385b17eed7f4ff0f6e82e60c3334ce7")
|
||||
);
|
||||
|
||||
executeTest("testPolyGTFreqUniform--" + testfile, spec);
|
||||
|
|
@ -69,7 +69,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(sampleGT + freqAF + "--variant " + testfile),
|
||||
1,
|
||||
Arrays.asList("3c1180fd9b5e80e540b39c5a95fbe722")
|
||||
Arrays.asList("0ee4a565a0d4f6b6942abd72a373becd")
|
||||
);
|
||||
|
||||
executeTest("testPolyGTFreqAF--" + testfile, spec);
|
||||
|
|
@ -81,7 +81,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(sampleGL + freqAF + "--variant " + testfile),
|
||||
1,
|
||||
Arrays.asList("ad30c028864348204ebe80b9c8c503e8")
|
||||
Arrays.asList("3bf094e1aef563daf7c936032259d490")
|
||||
);
|
||||
|
||||
executeTest("testPolyGLFreqAF--" + testfile, spec);
|
||||
|
|
|
|||
|
|
@ -304,7 +304,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
|
||||
" --comp:comp_genotypes " + testDir + "yri.trio.gatk.ug.head.vcf";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
|
||||
1, Arrays.asList("4b9dcbce0717285e3c0c736c1bed744c"));
|
||||
1, Arrays.asList("3cf734416452d953d433da6a3f418c3c"));
|
||||
executeTestParallel("testSelect1", spec);
|
||||
}
|
||||
|
||||
|
|
@ -332,7 +332,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testCompVsEvalAC() {
|
||||
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("659a15cc842f0310106fa595a26da71d"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("722ef452dede5d23038d10eca89d4f31"));
|
||||
executeTestParallel("testCompVsEvalAC",spec);
|
||||
}
|
||||
|
||||
|
|
@ -535,7 +535,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("f8460af997436a5ce4407fefb0e2724d")
|
||||
Arrays.asList("9236930cb26b01a9b9d770b0f048b182")
|
||||
);
|
||||
executeTest("testModernVCFWithLargeIndels", spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
|
|||
|
||||
VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
|
||||
"0ddd1e0e483d2eaf56004615cea23ec7", // tranches
|
||||
"a45a78de049cfe767ce23d3423f80b01", // recal file
|
||||
"6e1f98bb819ccf03e17a2288742160d3", // recal file
|
||||
"1050c387d170639f8cec221e5dddd626"); // cut VCF
|
||||
|
||||
@DataProvider(name = "VRTest")
|
||||
|
|
@ -75,7 +75,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
|
|||
|
||||
VRTest indel = new VRTest("combined.phase1.chr20.raw.indels.sites.vcf",
|
||||
"da4458d05f6396f5c4ab96f274e5ccdc", // tranches
|
||||
"918a5ecad5a2a8a46795144366683188", // recal file
|
||||
"8e2417336fa62e6c4d9f61b6deebdd82", // recal file
|
||||
"bf0e8ed5e250d52f0545074c61217d16"); // cut VCF
|
||||
|
||||
@DataProvider(name = "VRIndelTest")
|
||||
|
|
@ -133,7 +133,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
|
|||
" -o %s" +
|
||||
" -tranchesFile " + testDir + "VQSR.mixedTest.tranches" +
|
||||
" -recalFile " + testDir + "VQSR.mixedTest.recal",
|
||||
Arrays.asList("9039576b63728df7ee2c881817c0e9eb"));
|
||||
Arrays.asList("1370d7701a6231633d43a8062b7aff7f"));
|
||||
executeTest("testApplyRecalibrationSnpAndIndelTogether", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -78,26 +78,26 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
|
|||
executeTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
|
||||
}
|
||||
|
||||
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "c1e82f0842ca721d10f21604f26a5248"); }
|
||||
@Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "b2fcf3983cc9e667b9bbed8372080776", " -setKey foo"); }
|
||||
@Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "98c0cbb94e5debf7545a656665a1b659", " -setKey null"); }
|
||||
@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "10170f9e72cc831a5820bd03e70fe46a"); } // official project VCF files in tabix format
|
||||
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "d406bdc37f85d69cb3bf11a173399078"); }
|
||||
@Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "f780b4f5b424d9c85fc923004ec830ef", " -setKey foo"); }
|
||||
@Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "e93fdfaf8667b433dfe918ddc4134df2", " -setKey null"); }
|
||||
@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "253d44579b9d726c4700fd1f3a80b857"); } // official project VCF files in tabix format
|
||||
|
||||
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "074e909f80ffcc9fddc3fac89ea36bef"); }
|
||||
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f26980af214011c0452b8ce843f3063b"); }
|
||||
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "adf8f5a11fe0dce021c32938ecc8125b"); }
|
||||
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "8e5826184e4999f8639918b443e863ee"); }
|
||||
|
||||
@Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "5bc1de1197506aced0f9e7a08b572c44"); }
|
||||
@Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "9596b94b3506923109d877b255be78c4"); }
|
||||
|
||||
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "06e86711bcf0efc0f0c4a378f6147cf6"); } // official project VCF files in tabix format
|
||||
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "03103f6b39e9fb7a396df0013f01fae6"); } // official project VCF files in tabix format
|
||||
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "12fc1b8145f7884762f0c2cbbd319ae1"); }
|
||||
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "bc09ce3328339268838ec4e0819c940a"); } // official project VCF files in tabix format
|
||||
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "848d4408ee953053d2307cefebc6bd6d"); } // official project VCF files in tabix format
|
||||
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "06cd6666003cea545c21948bdec0ac39"); }
|
||||
|
||||
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "7e2dba80ba38b2a86713f635d630eb59"); }
|
||||
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "a66fbe674c7de0ecaeb0d3062393bfae"); }
|
||||
|
||||
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "3950392e1b8b53ae363e705185ad1da9"); }
|
||||
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "7f9272950475fe0c95c00752510456eb"); }
|
||||
|
||||
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "5c60eb8d5d4b957a0cf52ca008f021ba"); }
|
||||
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "774b43e69cc7ec93090b4f6e9f4a1079"); }
|
||||
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "def52bcd3942bbe39cd7ebe845c4f206"); }
|
||||
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "5f61145949180bf2a0cd342d8e064860"); }
|
||||
|
||||
@Test public void threeWayWithRefs() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
|
|
@ -110,7 +110,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
|
|||
" -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
|
||||
" -genotypeMergeOptions UNIQUIFY -L 1"),
|
||||
1,
|
||||
Arrays.asList("948291bbf47d1cec692d0fe4358ff92c"));
|
||||
Arrays.asList("90fa9f9b73fd10291e8067ecf7757b8d"));
|
||||
executeTest("threeWayWithRefs", spec);
|
||||
}
|
||||
|
||||
|
|
@ -127,17 +127,17 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
|
|||
executeTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
|
||||
}
|
||||
|
||||
@Test public void complexTestFull() { combineComplexSites("", "dd805f6edfc3cf724512dfbbe8df5183"); }
|
||||
@Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "14a205edb022f79abf1863588cfee56b"); }
|
||||
@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "e118d04d1d47c02ad38c046561a9f616"); }
|
||||
@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "e118d04d1d47c02ad38c046561a9f616"); }
|
||||
@Test public void complexTestFull() { combineComplexSites("", "69da09747b0d02e516672dd1f36d9f2f"); }
|
||||
@Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "4d1e0c12d95f50e472493fc14af3cc06"); }
|
||||
@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "9a98b01b9b2a28ae6af3125edc131dea"); }
|
||||
@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "9a98b01b9b2a28ae6af3125edc131dea"); }
|
||||
|
||||
@Test
|
||||
public void combineDBSNPDuplicateSites() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T CombineVariants --no_cmdline_in_header -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132,
|
||||
1,
|
||||
Arrays.asList("a838dc241cf357466cd4331fd298c73a"));
|
||||
Arrays.asList("3d2a5a43db86e3f6217ed2a63251285b"));
|
||||
executeTest("combineDBSNPDuplicateSites:", spec);
|
||||
}
|
||||
}
|
||||
|
|
@ -40,7 +40,7 @@ public class LeftAlignVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + testDir + "forLeftAlignVariantsTest.vcf --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("8e0991576518823b339a4e2f83299d4f"));
|
||||
Arrays.asList("bcf05f56adbb32a47b6d6b27b327d5c2"));
|
||||
executeTest("test left alignment", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("9fb54ed003234a5847c565ffb6767b95")
|
||||
Arrays.asList("133fd0ded0bb213097cbe68995afbb7e")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
|
||||
|
|
@ -31,7 +31,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(" -sn A -sn B -sn C --variant " + testfile),
|
||||
1,
|
||||
Arrays.asList("77579c53dbde4e8171f3cee83b98351b")
|
||||
Arrays.asList("1024d7d1e563c56c2c667f98b1b81028")
|
||||
);
|
||||
|
||||
executeTest("testRepeatedLineSelection--" + testfile, spec);
|
||||
|
|
@ -44,7 +44,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("03abdc27bfd7aa36d57bba0325b31e0d")
|
||||
Arrays.asList("f64c90c4cca470f1095d9fa2062eac3e")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
|
||||
|
|
@ -59,7 +59,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
|
||||
1,
|
||||
Arrays.asList("6cd82274335eeb0b449e571f38d54d3a")
|
||||
Arrays.asList("357c26f0a57f9d59a3bfca168af4fe42")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testComplexSelection--" + testfile, spec);
|
||||
|
|
@ -73,7 +73,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile,
|
||||
1,
|
||||
Arrays.asList("bbd7b28d1c5701e17b395d64f8b6f13d")
|
||||
Arrays.asList("34e714c7469b3cf5bf910222baff4cd0")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
|
||||
|
|
@ -88,7 +88,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc " + b37hapmapGenotypes + " --variant " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("76857b016198c3e08a2e27bbdb49f3f0")
|
||||
Arrays.asList("9da5dab3d344c1c0a5987b15e60fa082")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
|
||||
|
|
@ -102,7 +102,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("6c0b0c5f03d26f4a7a1438a2afc9fb6b")
|
||||
Arrays.asList("30b89b3a6706f7f46b23bfb3be69cc8e")
|
||||
);
|
||||
|
||||
executeTest("testVariantTypeSelection--" + testFile, spec);
|
||||
|
|
@ -115,7 +115,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("a8a26c621018142c9cba1080cbe687a8")
|
||||
Arrays.asList("4eeab0dd18712d0ca5ebe77c24ec989f")
|
||||
);
|
||||
|
||||
executeTest("testUsingDbsnpName--" + testFile, spec);
|
||||
|
|
@ -128,7 +128,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("6bee6dc2316aa539560a6d9d8adbc4ff")
|
||||
Arrays.asList("5bf9663274ceb552f5469f8c1dfc22ed")
|
||||
);
|
||||
|
||||
executeTest("testRegenotype--" + testFile, spec);
|
||||
|
|
@ -141,7 +141,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("6ff686a64e98fc1be2cde9b034d4a43a")
|
||||
Arrays.asList("cb9932f9a7aa2e53af605b30d88ad43f")
|
||||
);
|
||||
|
||||
executeTest("testMultipleRecordsAtOnePosition--" + testFile, spec);
|
||||
|
|
@ -154,7 +154,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
|
||||
1,
|
||||
Arrays.asList("95c4d43b11c3d0dd3ab19941c474269b")
|
||||
Arrays.asList("920605cc2182026e3f54c009f6a04141")
|
||||
);
|
||||
|
||||
executeTest("testNoGTs--" + testFile, spec);
|
||||
|
|
@ -169,7 +169,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
spec = new WalkerTestSpec(
|
||||
baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 2"),
|
||||
1,
|
||||
Arrays.asList("6cd82274335eeb0b449e571f38d54d3a")
|
||||
Arrays.asList("357c26f0a57f9d59a3bfca168af4fe42")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testParallelization (2 threads)--" + testfile, spec);
|
||||
|
|
@ -183,7 +183,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
spec = new WalkerTestSpec(
|
||||
baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 4"),
|
||||
1,
|
||||
Arrays.asList("6cd82274335eeb0b449e571f38d54d3a")
|
||||
Arrays.asList("357c26f0a57f9d59a3bfca168af4fe42")
|
||||
);
|
||||
spec.disableShadowBCF();
|
||||
|
||||
|
|
@ -197,7 +197,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile,
|
||||
1,
|
||||
Arrays.asList("fa92b3b41f1c04f685be8de32afc9706")
|
||||
Arrays.asList("e3d2e00dc7bfff85b87f78b6162ad333")
|
||||
);
|
||||
executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -83,7 +83,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
|
|||
" -GF RD" +
|
||||
" -o %s",
|
||||
1,
|
||||
Arrays.asList("f80c4714d83226b6a6db8bf281b3bcba"));
|
||||
Arrays.asList("d43562e9b94f0e8e337d38a6829671ee"));
|
||||
executeTest("testGenotypeFields", spec);
|
||||
}
|
||||
|
||||
|
|
@ -124,7 +124,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
|
|||
" --moltenize" +
|
||||
" -o %s",
|
||||
1,
|
||||
Arrays.asList("132890fd33d16946e04b41cfd7453c0e"));
|
||||
Arrays.asList("1d97fe63c249a995df4ce666382872d8"));
|
||||
executeTest("testMoltenOutputWithGenotypeFields", spec);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -19,7 +19,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testVariantsToVCFUsingDbsnpInput() {
|
||||
List<String> md5 = new ArrayList<String>();
|
||||
md5.add("a26afcce2a89f905a49c3d09719586b2");
|
||||
md5.add("268c116f825c2a4b5200a416ca587adc");
|
||||
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-R " + b36KGReference +
|
||||
|
|
@ -36,7 +36,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testVariantsToVCFUsingGeliInput() {
|
||||
List<String> md5 = new ArrayList<String>();
|
||||
md5.add("4accae035d271b35ee2ec58f403c68c6");
|
||||
md5.add("82ca5ecef2df5d64dee9ef5a4b14ef2f");
|
||||
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-R " + b36KGReference +
|
||||
|
|
@ -54,7 +54,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testGenotypesToVCFUsingGeliInput() {
|
||||
List<String> md5 = new ArrayList<String>();
|
||||
md5.add("2413f036ec4100b8d5db179946159a82");
|
||||
md5.add("90bc2e21d633fa6c3c47c6bd86c134a0");
|
||||
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-R " + b36KGReference +
|
||||
|
|
@ -72,7 +72,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testGenotypesToVCFUsingHapMapInput() {
|
||||
List<String> md5 = new ArrayList<String>();
|
||||
md5.add("f343085305e80c7a2493422e4eaad983");
|
||||
md5.add("bb71dabd072a679cc85fe8d3e130fb2b");
|
||||
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-R " + b36KGReference +
|
||||
|
|
@ -89,7 +89,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testGenotypesToVCFUsingVCFInput() {
|
||||
List<String> md5 = new ArrayList<String>();
|
||||
md5.add("b1ddde7efff9c405f8f92f0a636cd919");
|
||||
md5.add("ae39e2249bc20fcd0a668a7fe5fb84b0");
|
||||
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-R " + b36KGReference +
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ public class VCFIntegrationTest extends WalkerTest {
|
|||
@Test(enabled = true)
|
||||
public void testReadingAndWritingWitHNoChanges() {
|
||||
|
||||
String md5ofInputVCF = "ca5912c87813b21e980938fb75247bc6";
|
||||
String md5ofInputVCF = "babf02baabcfa7f72a2c6f7da5fdc996";
|
||||
String testVCF = testDir + "vcf4.1.example.vcf";
|
||||
|
||||
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
|
||||
|
|
@ -35,7 +35,7 @@ public class VCFIntegrationTest extends WalkerTest {
|
|||
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
|
||||
|
||||
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0cb81b9332fc21d03e74caff770b8a4a"));
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("d2604faad0613932453395c54cc68369"));
|
||||
executeTest("Test reading and writing breakpoint VCF", spec1);
|
||||
}
|
||||
|
||||
|
|
@ -46,7 +46,7 @@ public class VCFIntegrationTest extends WalkerTest {
|
|||
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
|
||||
|
||||
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("109bf9347965eb47706b4916bdd48a7a"));
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0807ff11bebba81b87a273ad6bee01a8"));
|
||||
executeTest("Test reading and writing samtools vcf", spec1);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue