Made TandemRepeatAnnotator standard annotation. HRun no longer standard (superceded by former)
This commit is contained in:
Guillermo del Angel
parent
d6df817174
commit
175bb35e70
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@ -19,7 +19,7 @@ import java.util.Map;
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/**
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* Largest contiguous homopolymer run of the variant allele in either direction on the reference. Computed only for bi-allelic sites.
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*/
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public class HomopolymerRun extends InfoFieldAnnotation implements StandardAnnotation {
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public class HomopolymerRun extends InfoFieldAnnotation {
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private boolean ANNOTATE_INDELS = true;
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@ -44,7 +44,7 @@ import java.util.List;
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import java.util.Map;
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public class TandemRepeatAnnotator extends InfoFieldAnnotation /*implements StandardAnnotation*/ {
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public class TandemRepeatAnnotator extends InfoFieldAnnotation implements StandardAnnotation {
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private static final String STR_PRESENT = "STR";
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private static final String REPEAT_UNIT_KEY = "RU";
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private static final String REPEATS_PER_ALLELE_KEY = "RPA";
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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("3b7796fa7c7dc94878bedadf7938db4c"));
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Arrays.asList("21810e5b51a0431b510a8d7a73f8771b"));
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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("2977bb30c8b84a5f4094fe6090658561"));
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Arrays.asList("31263a127c606f72fb00fac69f0320a6"));
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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: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("279cace364f747f9bae7fe391b5026f0"));
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Arrays.asList("bd367dbcbcc45cc43588e1d7309a7ad1"));
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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("0948cd1dba7d61f283cc4cf2a7757d92"));
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Arrays.asList("7f200756227a1ee75f33c466955015c5"));
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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("e488abd05d6162758698a3a7579866a6"));
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Arrays.asList("65dc85869239d52e3893e5ba47c1afac"));
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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("062155edec46a8c52243475fbf3a2943"));
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Arrays.asList("1d98be77dad9c703402de0315db5176a"));
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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("06635f2dd91b539bfbce9bf7914d8e43"));
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Arrays.asList("920d796cfaa19c20153181d7be627435"));
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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("820eeba1f6e3a0758a69d937c524a38e"));
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Arrays.asList("3a1e3ddd8c563a9de522c551e3d7e724"));
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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("cd7e3d43b8f5579c461b3e588a295fa8"));
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Arrays.asList("06107c9dfefc1ab53e366d0f86502ff2"));
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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("31cc2ce157dd20771418c08d6b3be1fa"));
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Arrays.asList("fe1e76a7a0d95ee7c604194b165a640d"));
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executeTest("getting DB tag with HM3", 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("074865f8f8c0ca7bfd58681f396c49e9"));
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Arrays.asList("b5583188347922476e23080a265c214e"));
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executeTest("using expression", spec);
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}
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@ -146,7 +146,7 @@ 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("97b26db8135d083566fb585a677fbe8a"));
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Arrays.asList("bb6d9553d6954923cdef157753735b87"));
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executeTest("using expression with ID", spec);
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}
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@ -30,7 +30,7 @@ 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("9b08dc6800ba11bc6d9f6ccf392a60fe"));
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Arrays.asList("0357f708cf93decd4fc2e66b59109fe1"));
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executeTest("test MultiSample Pilot1", spec);
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}
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@ -38,7 +38,7 @@ 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 " + testDir + "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("ea5b5dcea3a6eef7ec60070b551c994e"));
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Arrays.asList("b491ca7b74bbd010d3f3b3d571e3abf3"));
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executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
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}
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@ -46,7 +46,7 @@ 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 " + testDir + "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("1899bdb956c62bbcbf160b18cd3aea60"));
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Arrays.asList("981b8e3fef61a00c4df49e6429723e48"));
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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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@ -54,7 +54,7 @@ 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("d275e0f75368dbff012ea8655dce3444"));
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Arrays.asList("f178609d30230bbd3c0a4173f81c8d98"));
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executeTest("test SingleSample Pilot2", spec);
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}
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@ -62,7 +62,7 @@ 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 " + testDir + "multiallelic.snps.bam -o %s -L " + testDir + "multiallelic.snps.intervals", 1,
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Arrays.asList("ec907c65da5ed9b6046404b0f81422d4"));
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Arrays.asList("b4fd4daaa39373a4cc2ccca5320b4543"));
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executeTest("test Multiple SNP alleles", spec);
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}
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@ -70,7 +70,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testBadRead() {
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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 -I " + testDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
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Arrays.asList("7678827a2ee21870a41c09d28d26b996"));
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Arrays.asList("5eddd74df06bc5e9a5a629e039e03133"));
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executeTest("test bad read", spec);
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}
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@ -78,7 +78,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testReverseTrim() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
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Arrays.asList("a70593bbb5042e2d0e46e3c932cae170"));
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Arrays.asList("2695becb936f7fd680b067135c2cd2fc"));
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executeTest("test reverse trim", spec);
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}
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@ -88,7 +88,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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//
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// --------------------------------------------------------------------------------------------------------------
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private final static String COMPRESSED_OUTPUT_MD5 = "1e3c897794e5763a8720807686707b18";
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private final static String COMPRESSED_OUTPUT_MD5 = "0847bf352193e8ff52e3182e3f97db63";
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@Test
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public void testCompressedOutput() {
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@ -141,7 +141,7 @@ 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("258c1b33349eb3b2d395ec4d69302725"));
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Arrays.asList("d448aaa498337c9b15472aaa8137a98c"));
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executeTest("test min_base_quality_score 26", spec);
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}
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@ -149,7 +149,7 @@ 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("e9d23a08472e4e27b4f25e844f5bad57"));
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Arrays.asList("75250c65647acabcd0319820d67deffe"));
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executeTest("test SLOD", spec);
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}
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@ -157,7 +157,7 @@ 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("443b2f8882393c4c65277c34cdb6060c"));
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Arrays.asList("70d54bc2170f00ca1ddee45141a6a7e2"));
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executeTest("test NDA", spec);
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}
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@ -165,7 +165,7 @@ 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("71251d8893649ea9abd5d9aa65739ba1"));
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Arrays.asList("284d23c211f60dfac994e319caef0c36"));
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executeTest("test using comp track", spec);
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}
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@ -173,8 +173,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testOutputParameter() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( "-sites_only", "446ed9a72d210671ed48aa1f572b77e3" );
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e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "ecf92054c1e4bd9d6529b8002d385165" );
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e.put( "--output_mode EMIT_ALL_SITES", "e10819a2a7960254e27ed2b958b45d56" );
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e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "dd956beb4bb377a9b28e5da78df5f2f3" );
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e.put( "--output_mode EMIT_ALL_SITES", "a088df1f161f732ff148bd7a48894251" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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@ -188,7 +188,7 @@ 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("902327e8a45fe585c8dfd1a7c4fcf60f"));
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Arrays.asList("594e770c852a7e4a1dc2c4ab0065bebc"));
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executeTest("test confidence 1", spec1);
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}
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@ -196,7 +196,7 @@ 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("2343ac8113791f4e79643b333b34afc8"));
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Arrays.asList("ae52ac5a2c4515935294cddb5eadb255"));
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executeTest("test confidence 2", spec2);
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}
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@ -208,8 +208,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testHeterozyosity() {
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HashMap<Double, String> e = new HashMap<Double, String>();
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e.put( 0.01, "d07e5ca757fbcb1c03f652f82265c2f8" );
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e.put( 1.0 / 1850, "d1fb9186e6f39f2bcf5d0edacd8f7fe2" );
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e.put( 0.01, "fc1e160034b2beaa06f4edac06568d66" );
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e.put( 1.0 / 1850, "a64c9c16b22765edcfac261fd50b84e8" );
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for ( Map.Entry<Double, String> entry : e.entrySet() ) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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@ -233,7 +233,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -o %s" +
|
||||
" -L 1:10,000,000-10,100,000",
|
||||
1,
|
||||
Arrays.asList("623be1fd8b63a01bfe35ac864d5199fe"));
|
||||
Arrays.asList("db679044c22744067303939fef51a9d1"));
|
||||
|
||||
executeTest(String.format("test multiple technologies"), spec);
|
||||
}
|
||||
|
|
@ -252,7 +252,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
" -L 1:10,000,000-10,100,000" +
|
||||
" -baq CALCULATE_AS_NECESSARY",
|
||||
1,
|
||||
Arrays.asList("40ea10c0238c3be2991d31ae72476884"));
|
||||
Arrays.asList("ebd30ec778fbaf228458ac4a83210677"));
|
||||
|
||||
executeTest(String.format("test calling with BAQ"), spec);
|
||||
}
|
||||
|
|
@ -271,7 +271,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
" -o %s" +
|
||||
" -L 1:10,000,000-10,500,000",
|
||||
1,
|
||||
Arrays.asList("c9b0bd900a4ec949adfbd28909581eeb"));
|
||||
Arrays.asList("b3277e20f2368c2669ac5be46fafe513"));
|
||||
|
||||
executeTest(String.format("test indel caller in SLX"), spec);
|
||||
}
|
||||
|
|
@ -286,7 +286,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
" -minIndelCnt 1" +
|
||||
" -L 1:10,000,000-10,100,000",
|
||||
1,
|
||||
Arrays.asList("6b7c8691c527facf9884c2517d943f2f"));
|
||||
Arrays.asList("a67a040314113f649e3c2ffde326de4c"));
|
||||
|
||||
executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
|
||||
}
|
||||
|
|
@ -299,7 +299,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
" -o %s" +
|
||||
" -L 1:10,000,000-10,500,000",
|
||||
1,
|
||||
Arrays.asList("d72603aa33a086d64d4dddfd2995552f"));
|
||||
Arrays.asList("fa5b909790faaac329f2b6a19db6d628"));
|
||||
|
||||
executeTest(String.format("test indel calling, multiple technologies"), spec);
|
||||
}
|
||||
|
|
@ -309,7 +309,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
|
||||
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
|
||||
Arrays.asList("4a59fe207949b7d043481d7c1b786573"));
|
||||
Arrays.asList("c144a3a4d72cd281941ebf5e07d090f5"));
|
||||
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
|
||||
}
|
||||
|
||||
|
|
@ -319,7 +319,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
|
||||
+ testDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
|
||||
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
|
||||
Arrays.asList("a8a9ccf30bddee94bb1d300600794ee7"));
|
||||
Arrays.asList("af32437ec0ac6ea3b57196d163cac76e"));
|
||||
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
|
||||
}
|
||||
|
||||
|
|
@ -327,13 +327,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMultiSampleIndels() {
|
||||
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
|
||||
Arrays.asList("99e278baa2367b2bb016e2f37139d12f"));
|
||||
Arrays.asList("bce73149ce104fe91ff8e43db7faf27a"));
|
||||
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
|
||||
|
||||
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
|
||||
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
|
||||
Arrays.asList("c43ac445130161b8250bfbdc6c67782a"));
|
||||
Arrays.asList("822c7ed862a932deb59b16857e043404"));
|
||||
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
|
||||
}
|
||||
|
||||
|
|
@ -343,7 +343,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + testDir + vcf + " -I " + validationDataLocation +
|
||||
"NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1,
|
||||
Arrays.asList("7d069596597aee5e0d562964036141eb"));
|
||||
Arrays.asList("c56155e08b1264f289ed0c47d16a6cb4"));
|
||||
executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec);
|
||||
}
|
||||
|
||||
|
|
@ -376,7 +376,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMinIndelFraction0() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
assessMinIndelFraction + " -minIndelFrac 0.0", 1,
|
||||
Arrays.asList("1e4595c85159bd9b62eff575134b5dd9"));
|
||||
Arrays.asList("f4783e6ba325500466a9f6ca9b7a4a7c"));
|
||||
executeTest("test minIndelFraction 0.0", spec);
|
||||
}
|
||||
|
||||
|
|
@ -384,7 +384,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMinIndelFraction25() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
assessMinIndelFraction + " -minIndelFrac 0.25", 1,
|
||||
Arrays.asList("6d9dbb949626fdb0bca6a7904e9b0c1f"));
|
||||
Arrays.asList("c0551a6a3d3eb598d2b35866e396e836"));
|
||||
executeTest("test minIndelFraction 0.25", spec);
|
||||
}
|
||||
|
||||
|
|
@ -392,7 +392,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMinIndelFraction100() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
assessMinIndelFraction + " -minIndelFrac 1", 1,
|
||||
Arrays.asList("a31a355bc2b8257b2a45494e97322694"));
|
||||
Arrays.asList("306296493ba67e425250f31606210806"));
|
||||
executeTest("test minIndelFraction 1.0", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue