Update MD5s with new FS score
This commit is contained in:
Mark DePristo
parent
4b8d9c3915
commit
0f4acaae1b
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@ -47,12 +47,12 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
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@Test(enabled = true)
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public void testBOTH_GGA_Pools() {
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PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","077db83cf7dc5490f670c85856b408b2");
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PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","0ff90fa3882a3fb5089a7bba50dd8ae3");
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}
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@Test(enabled = true)
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public void testINDEL_GGA_Pools() {
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PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","e460a17377b731ff4eab36fb56042ecd");
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PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","90af837f372e3d5143af30bf5c8c2b75");
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}
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@Test(enabled = true)
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@ -67,11 +67,11 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
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@Test(enabled = true)
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public void testMT_SNP_DISCOVERY_sp4() {
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PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","da359fe7dd6dce045193198c264301ee");
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PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","c32e10070e10d30d33e5b882c1f89413");
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}
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@Test(enabled = true)
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public void testMT_SNP_GGA_sp10() {
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PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "ad0eef3a9deaa098d79df62af7e5448a");
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PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "4d16d3c9475637bad70e9dc2eafe2da2");
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}
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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 " + privateTestDir + "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("4a0318d0452d2dccde48ef081c431bf8"));
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Arrays.asList("fbfbd4d13b7ba3d76e8e186902e81378"));
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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 " + privateTestDir + "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("da19c8e3c58340ba8bcc88e95ece4ac1"));
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Arrays.asList("19aef8914efc497192f89a9038310ca5"));
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executeTest("test file has annotations, 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 " + privateTestDir + "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("cdefe79f46482a3d050ca2132604663a"));
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Arrays.asList("4f0b8033da18e6cf6e9b8d5d36c21ba2"));
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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 " + privateTestDir + "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("5ec4c07b6801fca7013e3b0beb8b5418"));
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Arrays.asList("64ca176d587dfa2b3b9dec9f7999305c"));
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executeTest("test file doesn't have annotations, asking for annotations, #2", 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 " + privateTestDir + "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("28c07151f5c5fae87c691d8f7d1a3929"));
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Arrays.asList("0c810f6c4abef9d9dc5513ca872d3d22"));
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executeTest("test overwriting header", spec);
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}
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@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot1() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
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Arrays.asList("9a7fa3e9ec8350e3e9cfdce0c00ddcc3"));
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Arrays.asList("cafd404f1b4f53586f7aa7a7084b91da"));
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executeTest("test MultiSample Pilot1", spec);
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}
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@ -36,7 +36,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testWithAllelesPassedIn1() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
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Arrays.asList("78693f3bf5d588e250507a596aa400da"));
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Arrays.asList("9a760dffbb299bda4934bcb4f7aad42a"));
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executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
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}
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@ -44,7 +44,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testWithAllelesPassedIn2() {
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
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Arrays.asList("babf24ec8e5b5708d4a049629f7ea073"));
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Arrays.asList("8391146877aa7801ffdb3aa954bf2965"));
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executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
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}
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@ -52,7 +52,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testSingleSamplePilot2() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
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Arrays.asList("754187e70c1d117087e2270950a1c230"));
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Arrays.asList("85b79ff7910f218dd59595d03ffe6ccc"));
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executeTest("test SingleSample Pilot2", spec);
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}
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@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultipleSNPAlleles() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
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Arrays.asList("f9a2f882d050a90e6d8e6a1fba00f858"));
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Arrays.asList("8472b1ad2fe1060e732da9e29d10cf99"));
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executeTest("test Multiple SNP alleles", spec);
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}
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@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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//
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// --------------------------------------------------------------------------------------------------------------
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private final static String COMPRESSED_OUTPUT_MD5 = "ebb42960e115fb8dacd3edff5541b4da";
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private final static String COMPRESSED_OUTPUT_MD5 = "712e87db5e278e92bd36e96d377303c6";
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@Test
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public void testCompressedOutput() {
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@ -139,7 +139,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMinBaseQualityScore() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1,
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Arrays.asList("91f7e112200ed2c3b0a5d0d9e16e9369"));
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Arrays.asList("f73dec2e77f14c170f7b6a8eee5793ff"));
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executeTest("test min_base_quality_score 26", spec);
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}
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@ -147,7 +147,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testSLOD() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
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Arrays.asList("b86e52b18496ab43a6b9a1bda632b5e6"));
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Arrays.asList("da7a5a3aa1c9f401896c34199c535954"));
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executeTest("test SLOD", spec);
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}
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@ -155,7 +155,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testNDA() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
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Arrays.asList("79b3e4f8b4476ce3c3acbc271d6ddcdc"));
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Arrays.asList("07f5962f790673a1299f3a0f56579b65"));
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executeTest("test NDA", spec);
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}
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@ -163,23 +163,23 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testCompTrack() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
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Arrays.asList("bf7f21a600956eda0a357b97b21e3069"));
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Arrays.asList("22037eac40a3b1df3086c2d7b27f0d5f"));
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executeTest("test using comp track", spec);
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}
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@Test
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public void testOutputParameterSitesOnly() {
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testOutputParameters("-sites_only", "976109543d8d97d94e0fe0521ff326e8");
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testOutputParameters("-sites_only", "92db524b334f1416e595c711abc2d798");
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}
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@Test
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public void testOutputParameterAllConfident() {
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testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "bec7bcc50b42782e20a970db11201399");
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testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "da318257d25a02abd26a3348421c3c69");
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}
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@Test
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public void testOutputParameterAllSites() {
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testOutputParameters("--output_mode EMIT_ALL_SITES", "09494afd12cef97293ed35d1a972f623");
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testOutputParameters("--output_mode EMIT_ALL_SITES", "13c4f01cffbbfac600318be95b3ca02f");
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}
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private void testOutputParameters(final String args, final String md5) {
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@ -193,7 +193,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testConfidence() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
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Arrays.asList("e94be02fc5484c20b512840884e3d463"));
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Arrays.asList("7326eb84d8418546a408b68839a0a47e"));
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executeTest("test confidence 1", spec1);
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}
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@ -201,7 +201,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testConfidence2() {
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
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Arrays.asList("e94be02fc5484c20b512840884e3d463"));
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Arrays.asList("7326eb84d8418546a408b68839a0a47e"));
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executeTest("test confidence 2", spec2);
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}
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@ -212,12 +212,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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// --------------------------------------------------------------------------------------------------------------
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@Test
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public void testHeterozyosity1() {
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testHeterozosity( 0.01, "0dca2699f709793026b853c6f339bf08" );
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testHeterozosity( 0.01, "7aed8361e692eff559e6bca88752db0d" );
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}
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@Test
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public void testHeterozyosity2() {
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testHeterozosity( 1.0 / 1850, "35f14e436927e64712a8e28080e90c91" );
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testHeterozosity( 1.0 / 1850, "989e65bb7337117d31cd615163a8ac84" );
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}
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private void testHeterozosity(final double arg, final String md5) {
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@ -241,7 +241,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,100,000",
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1,
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Arrays.asList("0360b79163aa28ae66d0dde4c26b3d76"));
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Arrays.asList("c155587aa0410f43d7ccc57e1ae09a68"));
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executeTest(String.format("test multiple technologies"), spec);
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}
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@ -260,7 +260,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -L 1:10,000,000-10,100,000" +
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" -baq CALCULATE_AS_NECESSARY",
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1,
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Arrays.asList("59892388916bdfa544750ab76e43eabb"));
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Arrays.asList("0748a711c6154f8d85847afb79aead94"));
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executeTest(String.format("test calling with BAQ"), spec);
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}
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