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Merge pull request #1517 from broadinstitute/rhl_adapter_boundary_err_1406 

Fix adapter bounday for positive strand
This commit is contained in:
David Benjamin 2016-11-18 10:25:46 -05:00 committed by GitHub
parent 196675c0b2 22d94a7096
commit 055d653bc2
16 changed files with 131 additions and 130 deletions
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14
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
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@ -109,13 +109,13 @@ public class BQSRIntegrationTest extends WalkerTest {
@DataProvider(name = "BQSRTest") @DataProvider(name = "BQSRTest")
public Object[][] createBQSRTestData() { public Object[][] createBQSRTestData() {
return new Object[][]{ return new Object[][]{
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "fc9df1faf67bab70d32f89bcf4fa39db")}, {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "dde4269a873c6f7a751e775cbc79fdb9")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "73ec38eb23b1739ecef8194cbb1132a3")}, {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "fae427cb969638060e2294540e120dfc")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "2d5721193ed4410d1a7d8db467a1fa05")}, {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "651be7dcd798c71ceaefb773ed792193")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "16df7f1745f17f190c9fc33c475b91d8")}, {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "f5fd024e900d0d77c681483da1e5dfd5")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "01811003ae811ee74c4b8d3eb5e992fe")}, {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "751189ec8cd406628cf4e698c69e8d11")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "5e0eea6b0b300fbd2edabc3506ad3a60")}, {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "b921c36eb7f5be8f8b91b651247a83d7")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "8500b9747c16cb8eb17082163bdb8069")}, {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "6c3c6176eb6214dc7ef121fa11916e5d")},
{new BQSRTest(b36KGReference, SimpleCigarMatchMismatchBam, SimpleCigarMatchMismatchInterval, "", "56dfb2918a4cdae3ef9d705a43e85194")}, {new BQSRTest(b36KGReference, SimpleCigarMatchMismatchBam, SimpleCigarMatchMismatchInterval, "", "56dfb2918a4cdae3ef9d705a43e85194")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "0b5a8e259e997e4c7b5836d4c28e6f4d")}, {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "0b5a8e259e997e4c7b5836d4c28e6f4d")},
{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "281682124584ab384f23359934df0c3b")}, {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "281682124584ab384f23359934df0c3b")},

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java
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@ -62,7 +62,7 @@ public class ErrorRatePerCycleIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
"-T ErrorRatePerCycle -R " + b37KGReference + " -I " + b37GoodBAM + " -L 20:10,000,000-10,100,000 -o %s", "-T ErrorRatePerCycle -R " + b37KGReference + " -I " + b37GoodBAM + " -L 20:10,000,000-10,100,000 -o %s",
1, 1,
Arrays.asList("6191340f0b56ee81fb248c8f5c913a8e")); Arrays.asList("a83453820b7afb5ee79856093d62901f"));
executeTest("ErrorRatePerCycle:", spec); executeTest("ErrorRatePerCycle:", spec);
} }
} }

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
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@ -69,17 +69,17 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
@Test(enabled = true) @Test(enabled = true)
public void testSNP_ACS_Pools() { public void testSNP_ACS_Pools() {
executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "853b47780322b8133577aea528b9fd77"); executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "90ed6f1c268b9c57ecb52b35a88b9368");
} }
@Test(enabled = true) @Test(enabled = true)
public void testBOTH_GGA_Pools() { public void testBOTH_GGA_Pools() {
executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "ee5a2f8954f38d6e5d44fe50b22e43a1"); executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "5ad4dd6b0c3c170ba44fdad6d4fa58cf");
} }
@Test(enabled = true) @Test(enabled = true)
public void testINDEL_GGA_Pools() { public void testINDEL_GGA_Pools() {
executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "5cb3fe396302f3d4a4a9b7b3cc1877cc"); executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "d26b0ba07e056b73fe4cfe873636d0d6");
} }
@Test(enabled = true) @Test(enabled = true)

26
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinBaseQualityScore() { public void testMinBaseQualityScore() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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, 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,
Arrays.asList("52a3064863b97e43d8df878edc29275c")); Arrays.asList("d0499af17dc66e77849e547bc5a182ff"));
executeTest("test min_base_quality_score 26", spec); executeTest("test min_base_quality_score 26", spec);
} }
@ -102,7 +102,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testNDA() { public void testNDA() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("2f2d7dd623446fc3cae62a44a016c16d")); Arrays.asList("5f69de274c0705cf1cb9387651df98bf"));
executeTest("test NDA", spec); executeTest("test NDA", spec);
} }
@ -124,17 +124,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testOutputParameterSitesOnly() { public void testOutputParameterSitesOnly() {
testOutputParameters("-sites_only", "3c0e109190cfbe41d24e7726cc8fe6e3"); testOutputParameters("-sites_only", "4355f5b6fd8cd769a479677f1255bee5");
} }
@Test @Test
public void testOutputParameterAllConfident() { public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "06386b0a4495583aa924e5addd56c5dc"); testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "182af9490667cb6ce1415305de4f3fdd");
} }
@Test @Test
public void testOutputParameterAllSites() { public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "b8b21ad6a2ff1f908e8e0073b57ba0e0"); testOutputParameters("--output_mode EMIT_ALL_SITES", "524e85c225ce330fd094de93f078fa56");
} }
private void testOutputParameters(final String args, final String md5) { private void testOutputParameters(final String args, final String md5) {
@ -148,7 +148,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() { public void testConfidence() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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, 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,
Arrays.asList("5c7d237e666439edb0ef8c697e37933c")); Arrays.asList("c794c7681856c1ec3c3429dbd9e5dc75"));
executeTest("test confidence 1", spec1); executeTest("test confidence 1", spec1);
} }
@ -156,7 +156,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testNoPrior() { public void testNoPrior() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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 -inputPrior 0.33333 -inputPrior 0.33333", 1, 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 -inputPrior 0.33333 -inputPrior 0.33333", 1,
Arrays.asList("24b550bbc3c9f0577e069b3fd3122d52")); Arrays.asList("39d15f041a0c86058f46f23960bb129b"));
executeTest("test no prior 1", spec1); executeTest("test no prior 1", spec1);
} }
@ -165,7 +165,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testUserPrior() { public void testUserPrior() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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 -inputPrior 0.001 -inputPrior 0.495", 1, 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 -inputPrior 0.001 -inputPrior 0.495", 1,
Arrays.asList("f60b6705daec1059ce3e533bf8e44c89")); Arrays.asList("00bff7a5dc584b5b6931a826eae6b013"));
executeTest("test user prior 1", spec1); executeTest("test user prior 1", spec1);
} }
@ -174,7 +174,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void emitPLsAtAllSites() { public void emitPLsAtAllSites() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --output_mode EMIT_ALL_SITES -allSitePLs", 1, baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --output_mode EMIT_ALL_SITES -allSitePLs", 1,
Arrays.asList("ae778a64323abe0da5194f0b936f48aa")); Arrays.asList("afcb9c4fd4a0e9ba4694d911bc75a7b2"));
// GDA: TODO: BCF encoder/decoder doesn't seem to support non-standard values in genotype fields. IE even if there is a field defined in FORMAT and in the header the BCF2 encoder will still fail // GDA: TODO: BCF encoder/decoder doesn't seem to support non-standard values in genotype fields. IE even if there is a field defined in FORMAT and in the header the BCF2 encoder will still fail
spec1.disableShadowBCF(); spec1.disableShadowBCF();
@ -190,12 +190,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testHeterozyosity1() { public void testHeterozyosity1() {
testHeterozosity( 0.01, "7bbba110f720fc8c115fe2d53b34d693" ); testHeterozosity( 0.01, "8abbec54f4bf82d7c48bf40b43fdaa91" );
} }
@Test @Test
public void testHeterozyosity2() { public void testHeterozyosity2() {
testHeterozosity( 1.0 / 1850, "767e8eacd216ac7437456e690287cecf" ); testHeterozosity( 1.0 / 1850, "4221b00b0d10c005fb69fd2a298e384c" );
} }
private void testHeterozosity(final double arg, final String md5) { private void testHeterozosity(final double arg, final String md5) {
@ -274,7 +274,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" + " -o %s" +
" -L 1:10,000,000-10,100,000", " -L 1:10,000,000-10,100,000",
1, 1,
Arrays.asList("6464138c0bd2ab2cac06773f19e37a4c")); Arrays.asList("482f6b310e59d05508811932ec21c801"));
executeTest(String.format("test multiple technologies"), spec); executeTest(String.format("test multiple technologies"), spec);
} }
@ -293,7 +293,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" + " -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY", " -baq CALCULATE_AS_NECESSARY",
1, 1,
Arrays.asList("8885492069487efcf67e13608e762acd")); Arrays.asList("c99b7dbe881aa3274cb9876e495cf8f3"));
executeTest(String.format("test calling with BAQ"), spec); executeTest(String.format("test calling with BAQ"), spec);
} }

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
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@ -94,7 +94,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testSingleSamplePilot2() { public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1, baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList("e5c34be242c9b6bec687c7384ef83cb2")); Arrays.asList("5919639094d775cdd6b6965e1210753a"));
executeTest("test SingleSample Pilot2", spec); executeTest("test SingleSample Pilot2", spec);
} }
@ -102,7 +102,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testMultipleSNPAlleles() { public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1, "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
Arrays.asList("fca6cacfb523114a3fb93772569deb08")); Arrays.asList("3304a20af6745beeec07ef2c47d617d3"));
executeTest("test Multiple SNP alleles", spec); executeTest("test Multiple SNP alleles", spec);
} }
@ -126,7 +126,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testMismatchedPLs() { public void testMismatchedPLs() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1, "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
Arrays.asList("c41ff9e1e3cfb6bd45d772787dd8e2d3")); Arrays.asList("5dc0ccd66105e0f12c72987d56c85235"));
executeTest("test mismatched PLs", spec); executeTest("test mismatched PLs", spec);
} }
} }

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
View File

@ -72,7 +72,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test @Test
public void testHaplotypeCallerMultiSampleComplex1() { public void testHaplotypeCallerMultiSampleComplex1() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "79567a4e4307495e880e9782b3a88f7d"); HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "4f30d9c9f1eb4529071b7060e497235d");
} }
private void HCTestSymbolicVariants(String bam, String args, String md5) { private void HCTestSymbolicVariants(String bam, String args, String md5) {

44
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
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@ -87,11 +87,11 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
//TODO this might need to be addressed at some point. //TODO this might need to be addressed at some point.
//TODO the following test is commented out for the record //TODO the following test is commented out for the record
//tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "7f09c261950bf86e435edfa69ed2ec71"}); //tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "7f09c261950bf86e435edfa69ed2ec71"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "a4286ada7f9efaa83f7a8f0e72c3cb45"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "c87ff5438d4a6559b33970f1294f77c6"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "cf5545094ebb264fa8eb879fd848d9ef"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "2cc9f789100e138ffc0c383b12a1322a"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "0086cc735cf792a9f236ec057c73b750"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "44cc8f78e28d905efc30c218d821cc7c"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "2e81881e92061ad4eb29025ffdc129c7"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "2e81881e92061ad4eb29025ffdc129c7"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "2c67bdc08c8784f2114c2039270b9766"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "39b2ad53ffdfcbaa4af3454c321daaa7"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "861fa31b135d200f765914126b422cf4"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "861fa31b135d200f765914126b422cf4"});
return tests.toArray(new Object[][]{}); return tests.toArray(new Object[][]{});
@ -106,11 +106,11 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals; final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
// this functionality can be adapted to provide input data for whatever you might want in your data // this functionality can be adapted to provide input data for whatever you might want in your data
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3ae2c7e570855f6d6ca58ddd1089a970"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "cbf988eca3f368ef5b17108595cd8c5e"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "1961007bd98a174a4a1b3e76a9c2f156"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d146c8dc4fc0605b3776ab5fec837d53"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "b34b0b61583628fbd51221627adcdb81"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "c317193f0d1c9a8168f2625c8bf1dd2b"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "63ff771eed3e62340c8938b4963d0add"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "63ff771eed3e62340c8938b4963d0add"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1122a0b3849f42d1c4a654f93b660e1b"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "c6c19ff9dc229f6af6080a175267344c"});
final String NA12878bandedResolutionMD5 = "7240907ec3dc2ed49b55c9956546ba13"; final String NA12878bandedResolutionMD5 = "7240907ec3dc2ed49b55c9956546ba13";
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
@ -129,11 +129,11 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals; final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
// this functionality can be adapted to provide input data for whatever you might want in your data // this functionality can be adapted to provide input data for whatever you might want in your data
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "8bf132d73cf6b0851ae73c6799f19ba9"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "85749762dac9684f4c8f9da18a210109"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "654c8264cfcbcb71da479761912fbd71"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "6c727b804084a2324ecd1c98b72734b9"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "4959f20a8bd3327760d94ccc40157f81"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "190cef14684c95ba290d7a5fa13fdc07"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ad7855dbf6dda2060aa93a3ee010b3e"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ad7855dbf6dda2060aa93a3ee010b3e"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "50e628de2a79cd6887af020b713ca3b8"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "21c87a3edafee3cb080169963e1e2623"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e48bbcf453e63a6ea5eeda05f6865f94"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e48bbcf453e63a6ea5eeda05f6865f94"});
return tests.toArray(new Object[][]{}); return tests.toArray(new Object[][]{});
@ -147,11 +147,11 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals; final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
// this functionality can be adapted to provide input data for whatever you might want in your data // this functionality can be adapted to provide input data for whatever you might want in your data
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "6662cfc41393257dfd6c39f1af1e3843"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "532188686870c7edd2ea3352ea93f66a"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "dd9fdcae44ab316c04650bf50c38e4b2"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "48521b89cecceb9846e4dfc0dd415874"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cb318100ae15cb3dcc342b6142ac6361"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "eaacbeaff99a37ffa07e1f11e7f1deb2"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "af0fe243e3b96e59097187cd16ba1597"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "af0fe243e3b96e59097187cd16ba1597"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "8a094080fb25bbcd39325dcdd62bcf65"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "868a097a8a108f5159dbbabbfdb2e38b"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "685025831ac783784d7838e568e35f46"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "685025831ac783784d7838e568e35f46"});
return tests.toArray(new Object[][]{}); return tests.toArray(new Object[][]{});
@ -294,7 +294,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testNoCallGVCFMissingPLsBugFix() { public void testNoCallGVCFMissingPLsBugFix() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d", final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("66f242cf3f1f1776c743505b84505f94")); final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("883fdc6c10fd7cbc1de375ed26ce5734"));
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest("testNoCallGVCFMissingPLsBugFix", spec); executeTest("testNoCallGVCFMissingPLsBugFix", spec);
} }
@ -363,7 +363,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testHaplotypeCallerMultiAllelicNonRef() { public void testHaplotypeCallerMultiAllelicNonRef() {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -A StrandAlleleCountsBySample", final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -A StrandAlleleCountsBySample",
b37KGReference, privateTestDir + "multiallelic-nonref.bam", "2:47641259-47641859", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); b37KGReference, privateTestDir + "multiallelic-nonref.bam", "2:47641259-47641859", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("19fc2c5218d907fcdcd36de2afbef19c")); final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("7c707c66f77482e3f6b2b014b152bbf4"));
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest(" testHaplotypeCallerMultiAllelicNonRef", spec); executeTest(" testHaplotypeCallerMultiAllelicNonRef", spec);
} }
@ -372,7 +372,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testHaplotypeCallerMaxNumPLValues() { public void testHaplotypeCallerMaxNumPLValues() {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 70", final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 70",
b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("b2adc744d9dff2f488149bcc96d6bb6d")); final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("dd0bfade4f0a9f23a500fd23c3a24a29"));
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest("testHaplotypeCallerMaxNumPLValues", spec); executeTest("testHaplotypeCallerMaxNumPLValues", spec);
} }
@ -389,7 +389,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s", final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s",
b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals",
GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName); GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("cbd37b492f77c50d2da744d5e00c6f90")); final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5ea45f32c09e9f7a4132f98d642f260b"));
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel", spec); executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel", spec);
// Make sure the "Maximum allowed number of PLs exceeded" messages are in the log // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log
@ -414,7 +414,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s", final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s",
b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals",
GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName); GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("cbd37b492f77c50d2da744d5e00c6f90")); final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5ea45f32c09e9f7a4132f98d642f260b"));
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel", spec); executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel", spec);
// Make sure the "Maximum allowed number of PLs exceeded" messages are in the log // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log
@ -458,7 +458,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testHaplotypeCallerGVCSpanDel() { public void testHaplotypeCallerGVCSpanDel() {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L 1:26357667 -ERC GVCF --no_cmdline_in_header -A AS_ReadPosRankSumTest -A ReadPosRankSumTest -variant_index_type %s -variant_index_parameter %d", final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L 1:26357667 -ERC GVCF --no_cmdline_in_header -A AS_ReadPosRankSumTest -A ReadPosRankSumTest -variant_index_type %s -variant_index_parameter %d",
b37KGReference, privateTestDir + "NexPond-377866-1:26357600-26357700.bam", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); b37KGReference, privateTestDir + "NexPond-377866-1:26357600-26357700.bam", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("b8f0bb74bc099a8f78d600d88861e1b6")); final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("bb12cf2dfa6f1fa0692395e295792584"));
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest("testHaplotypeCallerGVCSpanDel", spec); executeTest("testHaplotypeCallerGVCSpanDel", spec);
} }

26
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -107,7 +107,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeBAMOutFlags() throws IOException { public void testHaplotypeBAMOutFlags() throws IOException {
HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "700c5d20e9d9d9a431fcda9bff91f72e", "a0daf5a80158d4a462248415c1e17565"); HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "2e4cd93b4cad12259728d19a41d2a6ff", "9d6bd79cdae3e3222fa93f542fbca153");
} }
@Test @Test
@ -118,7 +118,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeCallerSingleSample() throws IOException { public void testHaplotypeCallerSingleSample() throws IOException {
HCTest(NA12878_BAM, "", "c04293cb8466a1a217bce4ef419bdabe"); HCTest(NA12878_BAM, "", "9f17ce83e639a1bd9b3f2d9fa33b15b2");
} }
@Test @Test
@ -133,12 +133,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeCallerSingleSampleTetraploid() throws IOException { public void testHaplotypeCallerSingleSampleTetraploid() throws IOException {
HCTest(NA12878_BAM, "-ploidy 4", "5098645e8b570bc4521570654fa91806"); HCTest(NA12878_BAM, "-ploidy 4", "f993db900080aeb48c43982745e1084d");
} }
@Test @Test
public void testHaplotypeCallerMinBaseQuality() throws IOException { public void testHaplotypeCallerMinBaseQuality() throws IOException {
HCTest(NA12878_BAM, "-mbq 15", "c04293cb8466a1a217bce4ef419bdabe"); HCTest(NA12878_BAM, "-mbq 15", "9f17ce83e639a1bd9b3f2d9fa33b15b2");
} }
@Test @Test
@ -148,12 +148,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException { public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "5098645e8b570bc4521570654fa91806"); HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "f993db900080aeb48c43982745e1084d");
} }
@Test @Test
public void testHaplotypeCallerGraphBasedSingleSample() throws IOException { public void testHaplotypeCallerGraphBasedSingleSample() throws IOException {
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "8ab21bd6fb7ef37480f556fd5fa5375c"); HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "420954190aef671edd02bd3c73e22642");
} }
@Test @Test
@ -168,7 +168,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException { public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException {
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "ff8e142f491b06e17e64e3a5d59737a7"); HCTest(NA12878_BAM, "-D " + b37dbSNP132, "9e8513ed4065138bee8dd9363a9fd355");
} }
@Test @Test
@ -312,7 +312,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestDBSNPAnnotationWGS() { public void HCTestDBSNPAnnotationWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1, "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("b56895e6d28ea0b9dadeecd0ff61687e")); Arrays.asList("fc71471b01f93bc531e3cf19cdf78b1f"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
} }
@ -321,7 +321,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132 "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
+ " -L " + hg19Intervals + " -isr INTERSECTION", 1, + " -L " + hg19Intervals + " -isr INTERSECTION", 1,
Arrays.asList("7b52164df8bf76d789836f990bd6066a")); Arrays.asList("bf8bb5d13b01facdf90ec24bfbf82faa"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
} }
@ -329,7 +329,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestDBSNPAnnotationWGSGraphBased() { public void HCTestDBSNPAnnotationWGSGraphBased() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1, "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("096826325215f79fe70661d984ae45a4")); Arrays.asList("ec9a1fb56882c21f3e4793e5f71f4e9e"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
} }
@ -338,7 +338,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132 "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
+ " -L " + hg19Intervals + " -isr INTERSECTION", 1, + " -L " + hg19Intervals + " -isr INTERSECTION", 1,
Arrays.asList("ff3b24412090ce7693d66d750ae84ac9")); Arrays.asList("2ffaf2e9ef293a6d5ce7c00be40edba7"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
} }
@ -430,7 +430,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
// but please make sure that both outputs get the same variant, // but please make sure that both outputs get the same variant,
// alleles all with DBSNP ids // alleles all with DBSNP ids
// We test here that change in active region size does not have an effect in placement of indels. // We test here that change in active region size does not have an effect in placement of indels.
final String md5 = "87b687b5476eb38b11db6a156b4066c8"; final String md5 = "66caceac0a54cdfd847bfdf4226bb36a";
final WalkerTestSpec shortSpec = new WalkerTestSpec(commandLineShortInterval + " -o %s",Arrays.asList(md5)); final WalkerTestSpec shortSpec = new WalkerTestSpec(commandLineShortInterval + " -o %s",Arrays.asList(md5));
executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::shortInterval",shortSpec); executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::shortInterval",shortSpec);
final WalkerTestSpec longSpec = new WalkerTestSpec(commandLineLongInterval + " -o %s",Arrays.asList(md5)); final WalkerTestSpec longSpec = new WalkerTestSpec(commandLineLongInterval + " -o %s",Arrays.asList(md5));
@ -484,7 +484,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{ public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "2cf4cab0035d09aa0aec6f3faa2c9df6"); HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "408c6940a090d31c11c171ed5e0e033c");
} }
@Test @Test

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
View File

@ -69,7 +69,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
List<Object[]> tests = new ArrayList<>(); List<Object[]> tests = new ArrayList<>();
for ( final int nct : Arrays.asList(1, 2, 4) ) { for ( final int nct : Arrays.asList(1, 2, 4) ) {
tests.add(new Object[]{nct, "07f969acede5e0ad7e1e94f4383af2a9"}); tests.add(new Object[]{nct, "da195c6c4c8e765acb35f08e37132108"});
} }
return tests.toArray(new Object[][]{}); return tests.toArray(new Object[][]{});

8
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java
View File

@ -33,13 +33,13 @@ import java.util.Arrays;
public class CallableLociIntegrationTest extends WalkerTest { public class CallableLociIntegrationTest extends WalkerTest {
final static String commonArgs = "-R " + b36KGReference + " -T CallableLoci -I " + validationDataLocation + "/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s"; final static String commonArgs = "-R " + b36KGReference + " -T CallableLoci -I " + validationDataLocation + "/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s";
final static String SUMMARY_MD5 = "a6f5963669f19d9d137ced87d65834b0"; final static String SUMMARY_MD5 = "27aea9e76af554db5e886dacb0d3edd0";
@Test @Test
public void testCallableLociWalkerBed() { public void testCallableLociWalkerBed() {
String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -summary %s"; String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2, WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("9b4ffea1dbcfefadeb1c9fa74b0e0e59", SUMMARY_MD5)); Arrays.asList("908a22c0bfe81e6f4c571de290e48d03", SUMMARY_MD5));
executeTest("formatBed", spec); executeTest("formatBed", spec);
} }
@ -47,7 +47,7 @@ public class CallableLociIntegrationTest extends WalkerTest {
public void testCallableLociWalkerPerBase() { public void testCallableLociWalkerPerBase() {
String gatk_args = commonArgs + " -format STATE_PER_BASE -L 1:10,000,000-11,000,000 -summary %s"; String gatk_args = commonArgs + " -format STATE_PER_BASE -L 1:10,000,000-11,000,000 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2, WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("d6505e489899e80c08a7168777f6e07b", SUMMARY_MD5)); Arrays.asList("11e7fdd39bb83eec44ca452faf0dc825", SUMMARY_MD5));
executeTest("format_state_per_base", spec); executeTest("format_state_per_base", spec);
} }
@ -63,7 +63,7 @@ public class CallableLociIntegrationTest extends WalkerTest {
public void testCallableLociWalker3() { public void testCallableLociWalker3() {
String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -minDepth 10 -maxDepth 100 --minBaseQuality 10 --minMappingQuality 20 -summary %s"; String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -minDepth 10 -maxDepth 100 --minBaseQuality 10 --minMappingQuality 20 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2, WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("7f79ad8195c4161060463eeb21d2bb11", "7ee269e5f4581a924529a356cc806e55")); Arrays.asList("5e5ee8850815810680f205a520d05a0f", "441b7c31bed5c30705f9565b708ecace"));
executeTest("formatBed lots of arguments", spec); executeTest("formatBed lots of arguments", spec);
} }
} }

26
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java
View File

@ -84,25 +84,25 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
spec.setOutputFileLocation(baseOutputFile); spec.setOutputFileLocation(baseOutputFile);
// now add the expected files that get generated // now add the expected files that get generated
spec.addAuxFile("0f9603eb1ca4a26828e82d8c8f4991f6", baseOutputFile); spec.addAuxFile("423571e4c05e7934322172654ac6dbb7", baseOutputFile);
spec.addAuxFile("51e6c09a307654f43811af35238fb179", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts")); spec.addAuxFile("9df5e7e07efeb34926c94a724714c219", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
spec.addAuxFile("3bf1d7247ea68d1afb35c2032c68dbdf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions")); spec.addAuxFile("3bf1d7247ea68d1afb35c2032c68dbdf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics")); spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
spec.addAuxFile("681dcbedcf7ca14bb44134abd1d8da3f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); spec.addAuxFile("31f9aa7ddad7809bc2f6675014dd4eaf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
spec.addAuxFile("0f58e7f0909b84897fea5daebd9d2948", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics")); spec.addAuxFile("958667ce6f92106a32a77098c1533d4f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
spec.addAuxFile("2832e48c12b1d8811ccd319a8ffb8dc1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary")); spec.addAuxFile("5e87db30702e44031920f7417cfac844", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
spec.addAuxFile("a836b92ac17b8ff9788e2aaa9116b5d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts")); spec.addAuxFile("b82846df660f0aac8429aec57c2a62d6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
spec.addAuxFile("22fee04ffca7fa489ae2e66309de12e4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions")); spec.addAuxFile("22fee04ffca7fa489ae2e66309de12e4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics")); spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
spec.addAuxFile("2de22ad840bf40621e51316728a32fe9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); spec.addAuxFile("e0f0d44cb4bc0557ee55b8b2aaa0cb9f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
spec.addAuxFile("6c84a067016c63e8c2face2de800acc7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); spec.addAuxFile("d69d08fd37f63941eea52d7b66a625df", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
spec.addAuxFile("2629883b99428f51e2d90d820b45504a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); spec.addAuxFile("de1795f42397d1282c012a3b9c396b5c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
spec.addAuxFile("6909d50a7da337cd294828b32b945eb8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); spec.addAuxFile("d53431022f7387fe9ac47814ab1fcd88", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
spec.addAuxFile("f6e52c5659f53afdcfc69c25272b9e99", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); spec.addAuxFile("f6e52c5659f53afdcfc69c25272b9e99", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
spec.addAuxFile("c2fb3a31d02df03c35afbe7f2284ad66", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); spec.addAuxFile("a72253b8e06dc6c653355b20e56e2f6e", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("d1b3d08c6e9565a1dab727d089085761", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); spec.addAuxFile("23ca7c647e3e53eb9b713d46b92bf6a2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("c0fadfcfd88cec81ba0d57b33bdec277", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); spec.addAuxFile("cd4ef2d43dc98f1bd7e6db532c60b3d1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
execute("testBaseOutputNoFiltering",spec); execute("testBaseOutputNoFiltering",spec);
} }

6
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java
View File

@ -77,10 +77,10 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
@DataProvider(name="GATKBAMIndexTest") @DataProvider(name="GATKBAMIndexTest")
public Object[][] makeMyDataProvider() { public Object[][] makeMyDataProvider() {
List<Object[]> tests = new ArrayList<Object[]>(); List<Object[]> tests = new ArrayList<Object[]>();
tests.add(new Object[]{"-L 20:1-76,050","8702701350de11a6d28204acefdc4775"}); tests.add(new Object[]{"-L 20:1-76,050","f275a2de053f44db19bc6591fe1c8dae"});
tests.add(new Object[]{"-L 20:10,000,000-10,001,100","818cf5a8229efe6f89fc1cd8145ccbe3"}); tests.add(new Object[]{"-L 20:10,000,000-10,001,100","818cf5a8229efe6f89fc1cd8145ccbe3"});
tests.add(new Object[]{"-L 20:62,954,114-63,025,520","22471ea4a12e5139aef62bf8ff2a5b63"}); tests.add(new Object[]{"-L 20:62,954,114-63,025,520","7e3462745d298de3b7493b42d3603392"});
tests.add(new Object[]{"-L 20:1-76,050 -L 20:20,000,000-20,000,100 -L 20:40,000,000-40,000,100 -L 20:30,000,000-30,000,100 -L 20:50,000,000-50,000,100 -L 20:62,954,114-63,025,520 ","08d899ed7c5a76ef3947bf67338acda1"}); tests.add(new Object[]{"-L 20:1-76,050 -L 20:20,000,000-20,000,100 -L 20:40,000,000-40,000,100 -L 20:30,000,000-30,000,100 -L 20:50,000,000-50,000,100 -L 20:62,954,114-63,025,520 ","977298255b04d66c17bb5466da8251f7"});
return tests.toArray(new Object[][]{}); return tests.toArray(new Object[][]{});
} }

2
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java
View File

@ -215,7 +215,7 @@ public class ReadUtils {
return read.getMateAlignmentStart() - 1; // case 1 (see header) return read.getMateAlignmentStart() - 1; // case 1 (see header)
} else { } else {
final int insertSize = Math.abs(read.getInferredInsertSize()); // the inferred insert size can be negative if the mate is mapped before the read (so we take the absolute value) final int insertSize = Math.abs(read.getInferredInsertSize()); // the inferred insert size can be negative if the mate is mapped before the read (so we take the absolute value)
return read.getAlignmentStart() + insertSize + 1; // case 2 (see header) return read.getAlignmentStart() + insertSize; // case 2 (see header)
} }
} }

83
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java
View File

@ -54,8 +54,8 @@ public class FragmentUtilsUnitTest extends BaseTest {
private final static boolean DEBUG = false; private final static boolean DEBUG = false;
private class FragmentUtilsTest extends TestDataProvider { private class FragmentUtilsTest extends TestDataProvider {
List<TestState> statesForPileup = new ArrayList<TestState>(); List<TestState> statesForPileup = new ArrayList<>();
List<TestState> statesForReads = new ArrayList<TestState>(); List<TestState> statesForReads = new ArrayList<>();
private FragmentUtilsTest(String name, int readLen, int leftStart, int rightStart, private FragmentUtilsTest(String name, int readLen, int leftStart, int rightStart,
boolean leftIsFirst, boolean leftIsNegative) { boolean leftIsFirst, boolean leftIsNegative) {
@ -70,8 +70,8 @@ public class FragmentUtilsUnitTest extends BaseTest {
boolean posCoveredByRight = pos >= right.getAlignmentStart() && pos <= right.getAlignmentEnd(); boolean posCoveredByRight = pos >= right.getAlignmentStart() && pos <= right.getAlignmentEnd();
if ( posCoveredByLeft || posCoveredByRight ) { if ( posCoveredByLeft || posCoveredByRight ) {
List<GATKSAMRecord> reads = new ArrayList<GATKSAMRecord>(); List<GATKSAMRecord> reads = new ArrayList<>();
List<Integer> offsets = new ArrayList<Integer>(); List<Integer> offsets = new ArrayList<>();
if ( posCoveredByLeft ) { if ( posCoveredByLeft ) {
reads.add(left); reads.add(left);
@ -174,7 +174,7 @@ public class FragmentUtilsUnitTest extends BaseTest {
@DataProvider(name = "MergeFragmentsTest") @DataProvider(name = "MergeFragmentsTest")
public Object[][] createMergeFragmentsTest() throws Exception { public Object[][] createMergeFragmentsTest() throws Exception {
List<Object[]> tests = new ArrayList<Object[]>(); List<Object[]> tests = new ArrayList<>();
final String leftFlank = "CCC"; final String leftFlank = "CCC";
final String rightFlank = "AAA"; final String rightFlank = "AAA";
@ -248,29 +248,29 @@ public class FragmentUtilsUnitTest extends BaseTest {
final byte[] commonQuals = Utils.dupBytes((byte)30, common.length()); final byte[] commonQuals = Utils.dupBytes((byte)30, common.length());
final String adapter = "NNNN"; final String adapter = "NNNN";
final GATKSAMRecord read1 = makeOverlappingRead(adapter, 30, common, commonQuals, "", 30, 10); final GATKSAMRecord readLeftAdapter = makeOverlappingRead(adapter, 30, common, commonQuals, "", 30, 10);
final GATKSAMRecord read2 = makeOverlappingRead("", 30, common, commonQuals, adapter, 30, 10); final GATKSAMRecord readRightAdapter = makeOverlappingRead("", 30, common, commonQuals, adapter, 30, 10);
final GATKSAMRecord expectedMerged = makeOverlappingRead("", 30, common, commonQuals, "", 30, 10); final GATKSAMRecord expectedMerged = makeOverlappingRead("", 30, common, commonQuals, "", 30, 10);
read1.setCigarString("4S" + common.length() + "M"); readLeftAdapter.setCigarString(adapter.length() + "S" + common.length() + "M");
read1.setProperPairFlag(true); readLeftAdapter.setProperPairFlag(true);
read1.setReadPairedFlag(true); readLeftAdapter.setReadPairedFlag(true);
read1.setFirstOfPairFlag(true); readLeftAdapter.setFirstOfPairFlag(true);
read1.setReadNegativeStrandFlag(true); readLeftAdapter.setReadNegativeStrandFlag(true);
read1.setMateNegativeStrandFlag(false); readLeftAdapter.setMateNegativeStrandFlag(false);
read1.setMateAlignmentStart(read2.getAlignmentStart()); readLeftAdapter.setMateAlignmentStart(readRightAdapter.getAlignmentStart());
read2.setCigarString(common.length() + "M4S"); readRightAdapter.setCigarString(common.length() + "M4S");
read2.setProperPairFlag(true); readRightAdapter.setProperPairFlag(true);
read2.setReadPairedFlag(true); readRightAdapter.setReadPairedFlag(true);
read2.setFirstOfPairFlag(false); readRightAdapter.setFirstOfPairFlag(false);
read2.setReadNegativeStrandFlag(false); readRightAdapter.setReadNegativeStrandFlag(false);
read2.setMateNegativeStrandFlag(true); readRightAdapter.setMateNegativeStrandFlag(true);
read2.setMateAlignmentStart(read1.getAlignmentStart()); readRightAdapter.setMateAlignmentStart(readLeftAdapter.getAlignmentStart());
final int insertSize = common.length() - 1; final int insertSize = common.length();
read1.setInferredInsertSize(-insertSize); readLeftAdapter.setInferredInsertSize(-insertSize);
read2.setInferredInsertSize(insertSize); readRightAdapter.setInferredInsertSize(insertSize);
final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(read1, read2); final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(readLeftAdapter, readRightAdapter);
Assert.assertEquals(actual.getCigarString(), expectedMerged.getCigarString()); Assert.assertEquals(actual.getCigarString(), expectedMerged.getCigarString());
Assert.assertEquals(actual.getReadBases(), expectedMerged.getReadBases()); Assert.assertEquals(actual.getReadBases(), expectedMerged.getReadBases());
Assert.assertEquals(actual.getReadGroup(), expectedMerged.getReadGroup()); Assert.assertEquals(actual.getReadGroup(), expectedMerged.getReadGroup());
@ -282,24 +282,25 @@ public class FragmentUtilsUnitTest extends BaseTest {
@Test(enabled = true) @Test(enabled = true)
public void testHardClippingBeforeMergeResultingInCompletelyContainedSecondRead() { public void testHardClippingBeforeMergeResultingInCompletelyContainedSecondRead() {
final String adapter = "NNNN"; final String adapter = "NNNN";
final int minReadSize = 7;
final GATKSAMRecord read1 = makeOverlappingRead(adapter, 30, Utils.dupString("A", 10), Utils.dupBytes((byte)30, 10), "", 30, 10); final GATKSAMRecord readLeftAdapter = makeOverlappingRead(adapter, 30, Utils.dupString("A", 10), Utils.dupBytes((byte)30, 10), "", 30, 10);
final GATKSAMRecord read2 = makeOverlappingRead("", 30, Utils.dupString("A", 7), Utils.dupBytes((byte)30, 7), adapter, 30, 10); final GATKSAMRecord readRightAdapter = makeOverlappingRead("", 30, Utils.dupString("A", minReadSize), Utils.dupBytes((byte)30, minReadSize), adapter, 30, 10);
read1.setCigarString("4S10M"); readLeftAdapter.setCigarString(adapter.length() + "S10M");
read1.setProperPairFlag(true); readLeftAdapter.setProperPairFlag(true);
read1.setFirstOfPairFlag(true); readLeftAdapter.setFirstOfPairFlag(true);
read1.setReadNegativeStrandFlag(true); readLeftAdapter.setReadNegativeStrandFlag(true);
read1.setMateAlignmentStart(10); readLeftAdapter.setMateAlignmentStart(10);
read2.setCigarString("7M4S"); readRightAdapter.setCigarString(minReadSize + "M4S");
read2.setProperPairFlag(true); readRightAdapter.setProperPairFlag(true);
read2.setFirstOfPairFlag(false); readRightAdapter.setFirstOfPairFlag(false);
read2.setReadNegativeStrandFlag(false); readRightAdapter.setReadNegativeStrandFlag(false);
final int insertSize = 7 - 1; final int insertSize = minReadSize;
read1.setInferredInsertSize(insertSize); readLeftAdapter.setInferredInsertSize(insertSize);
read2.setInferredInsertSize(-insertSize); readRightAdapter.setInferredInsertSize(-insertSize);
final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(read1, read2); final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(readLeftAdapter, readRightAdapter);
Assert.assertNull(actual); Assert.assertNull(actual);
} }
@ -356,7 +357,7 @@ public class FragmentUtilsUnitTest extends BaseTest {
@DataProvider(name = "AdjustFragmentsTest") @DataProvider(name = "AdjustFragmentsTest")
public Object[][] createAdjustFragmentsTest() throws Exception { public Object[][] createAdjustFragmentsTest() throws Exception {
List<Object[]> tests = new ArrayList<Object[]>(); List<Object[]> tests = new ArrayList<>();
final String leftFlank = "CCC"; final String leftFlank = "CCC";
final String rightFlank = "AAA"; final String rightFlank = "AAA";

4
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java
View File

@ -710,7 +710,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest {
read.setReadNegativeStrandFlag(false); read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true); read.setMateNegativeStrandFlag(true);
read.setMateAlignmentStart(start - 1); read.setMateAlignmentStart(start - 1);
read.setInferredInsertSize(goodBases - 1); read.setInferredInsertSize(goodBases);
tests.add(new Object[]{0, goodBases, nClips, read}); tests.add(new Object[]{0, goodBases, nClips, read});
} }
} }
@ -738,6 +738,6 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest {
} }
final int nExpectedPileups = nReadContainingPileups; final int nExpectedPileups = nReadContainingPileups;
Assert.assertEquals(nPileups, nExpectedPileups, "Wrong number of pileups seen"); Assert.assertEquals(nPileups, nExpectedPileups, "Wrong number of pileups seen for " + read + " with " + nClipsOnLeft + " clipped bases.");
} }
} }

4
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java
View File

@ -90,7 +90,7 @@ public class ReadUtilsUnitTest extends BaseTest {
read.setReadNegativeStrandFlag(false); read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true); read.setMateNegativeStrandFlag(true);
boundary = get.getAdaptor(read); boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, myStart + fragmentSize + 1); Assert.assertEquals(boundary, myStart + fragmentSize);
// Test case 2: positive strand, second read // Test case 2: positive strand, second read
read = makeRead(fragmentSize, mateStart); read = makeRead(fragmentSize, mateStart);
@ -99,7 +99,7 @@ public class ReadUtilsUnitTest extends BaseTest {
read.setReadNegativeStrandFlag(false); read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true); read.setMateNegativeStrandFlag(true);
boundary = get.getAdaptor(read); boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, myStart + fragmentSize + 1); Assert.assertEquals(boundary, myStart + fragmentSize);
// Test case 3: negative strand, second read // Test case 3: negative strand, second read
read = makeRead(fragmentSize, mateStart); read = makeRead(fragmentSize, mateStart);