zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
View File

@ -109,13 +109,13 @@ public class BQSRIntegrationTest extends WalkerTest {
@DataProvider(name = "BQSRTest")
public Object[][] createBQSRTestData() {
return new Object[][]{
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "fc9df1faf67bab70d32f89bcf4fa39db")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "73ec38eb23b1739ecef8194cbb1132a3")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "2d5721193ed4410d1a7d8db467a1fa05")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "16df7f1745f17f190c9fc33c475b91d8")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "01811003ae811ee74c4b8d3eb5e992fe")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "5e0eea6b0b300fbd2edabc3506ad3a60")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "8500b9747c16cb8eb17082163bdb8069")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "dde4269a873c6f7a751e775cbc79fdb9")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "fae427cb969638060e2294540e120dfc")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "651be7dcd798c71ceaefb773ed792193")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "f5fd024e900d0d77c681483da1e5dfd5")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "751189ec8cd406628cf4e698c69e8d11")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "b921c36eb7f5be8f8b91b651247a83d7")},
{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "6c3c6176eb6214dc7ef121fa11916e5d")},
{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 + "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
View File

@ -62,7 +62,7 @@ public class ErrorRatePerCycleIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T ErrorRatePerCycle -R " + b37KGReference + " -I " + b37GoodBAM + " -L 20:10,000,000-10,100,000 -o %s",
1,
Arrays.asList("6191340f0b56ee81fb248c8f5c913a8e"));
Arrays.asList("a83453820b7afb5ee79856093d62901f"));
executeTest("ErrorRatePerCycle:", spec);
}
}

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
View File

@ -69,17 +69,17 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
@Test(enabled = true)
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)
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)
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)

26
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinBaseQualityScore() {
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,
Arrays.asList("52a3064863b97e43d8df878edc29275c"));
Arrays.asList("d0499af17dc66e77849e547bc5a182ff"));
executeTest("test min_base_quality_score 26", spec);
}
@ -102,7 +102,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testNDA() {
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,
Arrays.asList("2f2d7dd623446fc3cae62a44a016c16d"));
Arrays.asList("5f69de274c0705cf1cb9387651df98bf"));
executeTest("test NDA", spec);
}
@ -124,17 +124,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameterSitesOnly() {
testOutputParameters("-sites_only", "3c0e109190cfbe41d24e7726cc8fe6e3");
testOutputParameters("-sites_only", "4355f5b6fd8cd769a479677f1255bee5");
}
@Test
public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "06386b0a4495583aa924e5addd56c5dc");
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "182af9490667cb6ce1415305de4f3fdd");
}
@Test
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) {
@ -148,7 +148,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
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,
Arrays.asList("5c7d237e666439edb0ef8c697e37933c"));
Arrays.asList("c794c7681856c1ec3c3429dbd9e5dc75"));
executeTest("test confidence 1", spec1);
}
@ -156,7 +156,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testNoPrior() {
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,
Arrays.asList("24b550bbc3c9f0577e069b3fd3122d52"));
Arrays.asList("39d15f041a0c86058f46f23960bb129b"));
executeTest("test no prior 1", spec1);
}
@ -165,7 +165,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testUserPrior() {
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,
Arrays.asList("f60b6705daec1059ce3e533bf8e44c89"));
Arrays.asList("00bff7a5dc584b5b6931a826eae6b013"));
executeTest("test user prior 1", spec1);
}
@ -174,7 +174,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void emitPLsAtAllSites() {
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,
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
spec1.disableShadowBCF();
@ -190,12 +190,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity1() {
testHeterozosity( 0.01, "7bbba110f720fc8c115fe2d53b34d693" );
testHeterozosity( 0.01, "8abbec54f4bf82d7c48bf40b43fdaa91" );
}
@Test
public void testHeterozyosity2() {
testHeterozosity( 1.0 / 1850, "767e8eacd216ac7437456e690287cecf" );
testHeterozosity( 1.0 / 1850, "4221b00b0d10c005fb69fd2a298e384c" );
}
private void testHeterozosity(final double arg, final String md5) {
@ -274,7 +274,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("6464138c0bd2ab2cac06773f19e37a4c"));
Arrays.asList("482f6b310e59d05508811932ec21c801"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -293,7 +293,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("8885492069487efcf67e13608e762acd"));
Arrays.asList("c99b7dbe881aa3274cb9876e495cf8f3"));
executeTest(String.format("test calling with BAQ"), spec);
}

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
View File

@ -94,7 +94,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testSingleSamplePilot2() {
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,
Arrays.asList("e5c34be242c9b6bec687c7384ef83cb2"));
Arrays.asList("5919639094d775cdd6b6965e1210753a"));
executeTest("test SingleSample Pilot2", spec);
}
@ -102,7 +102,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testMultipleSNPAlleles() {
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,
Arrays.asList("fca6cacfb523114a3fb93772569deb08"));
Arrays.asList("3304a20af6745beeec07ef2c47d617d3"));
executeTest("test Multiple SNP alleles", spec);
}
@ -126,7 +126,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testMismatchedPLs() {
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,
Arrays.asList("c41ff9e1e3cfb6bd45d772787dd8e2d3"));
Arrays.asList("5dc0ccd66105e0f12c72987d56c85235"));
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
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) {

44
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
View File

@ -87,11 +87,11 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
//TODO this might need to be addressed at some point.
//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, "a4286ada7f9efaa83f7a8f0e72c3cb45"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "cf5545094ebb264fa8eb879fd848d9ef"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "0086cc735cf792a9f236ec057c73b750"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "c87ff5438d4a6559b33970f1294f77c6"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "2cc9f789100e138ffc0c383b12a1322a"});
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.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"});
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;
// 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.BP_RESOLUTION, PCRFreeIntervals, "1961007bd98a174a4a1b3e76a9c2f156"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "b34b0b61583628fbd51221627adcdb81"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "cbf988eca3f368ef5b17108595cd8c5e"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d146c8dc4fc0605b3776ab5fec837d53"});
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.BP_RESOLUTION, WExIntervals, "1122a0b3849f42d1c4a654f93b660e1b"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "c6c19ff9dc229f6af6080a175267344c"});
final String NA12878bandedResolutionMD5 = "7240907ec3dc2ed49b55c9956546ba13";
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;
// 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.BP_RESOLUTION, PCRFreeIntervals, "654c8264cfcbcb71da479761912fbd71"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "4959f20a8bd3327760d94ccc40157f81"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "85749762dac9684f4c8f9da18a210109"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "6c727b804084a2324ecd1c98b72734b9"});
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.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"});
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;
// 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.BP_RESOLUTION, PCRFreeIntervals, "dd9fdcae44ab316c04650bf50c38e4b2"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cb318100ae15cb3dcc342b6142ac6361"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "532188686870c7edd2ea3352ea93f66a"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "48521b89cecceb9846e4dfc0dd415874"});
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.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"});
return tests.toArray(new Object[][]{});
@ -294,7 +294,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
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",
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();
executeTest("testNoCallGVCFMissingPLsBugFix", spec);
}
@ -363,7 +363,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
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",
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();
executeTest(" testHaplotypeCallerMultiAllelicNonRef", spec);
}
@ -372,7 +372,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
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",
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();
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",
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);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("cbd37b492f77c50d2da744d5e00c6f90"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5ea45f32c09e9f7a4132f98d642f260b"));
spec.disableShadowBCF();
executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel", spec);
// 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",
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);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("cbd37b492f77c50d2da744d5e00c6f90"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5ea45f32c09e9f7a4132f98d642f260b"));
spec.disableShadowBCF();
executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel", spec);
// 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() {
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);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("b8f0bb74bc099a8f78d600d88861e1b6"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("bb12cf2dfa6f1fa0692395e295792584"));
spec.disableShadowBCF();
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
public void testHaplotypeBAMOutFlags() throws IOException {
HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "700c5d20e9d9d9a431fcda9bff91f72e", "a0daf5a80158d4a462248415c1e17565");
HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "2e4cd93b4cad12259728d19a41d2a6ff", "9d6bd79cdae3e3222fa93f542fbca153");
}
@Test
@ -118,7 +118,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSample() throws IOException {
HCTest(NA12878_BAM, "", "c04293cb8466a1a217bce4ef419bdabe");
HCTest(NA12878_BAM, "", "9f17ce83e639a1bd9b3f2d9fa33b15b2");
}
@Test
@ -133,12 +133,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleTetraploid() throws IOException {
HCTest(NA12878_BAM, "-ploidy 4", "5098645e8b570bc4521570654fa91806");
HCTest(NA12878_BAM, "-ploidy 4", "f993db900080aeb48c43982745e1084d");
}
@Test
public void testHaplotypeCallerMinBaseQuality() throws IOException {
HCTest(NA12878_BAM, "-mbq 15", "c04293cb8466a1a217bce4ef419bdabe");
HCTest(NA12878_BAM, "-mbq 15", "9f17ce83e639a1bd9b3f2d9fa33b15b2");
}
@Test
@ -148,12 +148,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "5098645e8b570bc4521570654fa91806");
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "f993db900080aeb48c43982745e1084d");
}
@Test
public void testHaplotypeCallerGraphBasedSingleSample() throws IOException {
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "8ab21bd6fb7ef37480f556fd5fa5375c");
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "420954190aef671edd02bd3c73e22642");
}
@Test
@ -168,7 +168,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException {
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "ff8e142f491b06e17e64e3a5d59737a7");
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "9e8513ed4065138bee8dd9363a9fd355");
}
@Test
@ -312,7 +312,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestDBSNPAnnotationWGS() {
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,
Arrays.asList("b56895e6d28ea0b9dadeecd0ff61687e"));
Arrays.asList("fc71471b01f93bc531e3cf19cdf78b1f"));
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(
"-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,
Arrays.asList("7b52164df8bf76d789836f990bd6066a"));
Arrays.asList("bf8bb5d13b01facdf90ec24bfbf82faa"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
}
@ -329,7 +329,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestDBSNPAnnotationWGSGraphBased() {
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,
Arrays.asList("096826325215f79fe70661d984ae45a4"));
Arrays.asList("ec9a1fb56882c21f3e4793e5f71f4e9e"));
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(
"-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,
Arrays.asList("ff3b24412090ce7693d66d750ae84ac9"));
Arrays.asList("2ffaf2e9ef293a6d5ce7c00be40edba7"));
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,
// alleles all with DBSNP ids
// 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));
executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::shortInterval",shortSpec);
final WalkerTestSpec longSpec = new WalkerTestSpec(commandLineLongInterval + " -o %s",Arrays.asList(md5));
@ -484,7 +484,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
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

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<>();
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[][]{});

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 {
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
public void testCallableLociWalkerBed() {
String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("9b4ffea1dbcfefadeb1c9fa74b0e0e59", SUMMARY_MD5));
Arrays.asList("908a22c0bfe81e6f4c571de290e48d03", SUMMARY_MD5));
executeTest("formatBed", spec);
}
@ -47,7 +47,7 @@ public class CallableLociIntegrationTest extends WalkerTest {
public void testCallableLociWalkerPerBase() {
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,
Arrays.asList("d6505e489899e80c08a7168777f6e07b", SUMMARY_MD5));
Arrays.asList("11e7fdd39bb83eec44ca452faf0dc825", SUMMARY_MD5));
executeTest("format_state_per_base", spec);
}
@ -63,7 +63,7 @@ public class CallableLociIntegrationTest extends WalkerTest {
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";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("7f79ad8195c4161060463eeb21d2bb11", "7ee269e5f4581a924529a356cc806e55"));
Arrays.asList("5e5ee8850815810680f205a520d05a0f", "441b7c31bed5c30705f9565b708ecace"));
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);
// now add the expected files that get generated
spec.addAuxFile("0f9603eb1ca4a26828e82d8c8f4991f6", baseOutputFile);
spec.addAuxFile("51e6c09a307654f43811af35238fb179", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
spec.addAuxFile("423571e4c05e7934322172654ac6dbb7", baseOutputFile);
spec.addAuxFile("9df5e7e07efeb34926c94a724714c219", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
spec.addAuxFile("3bf1d7247ea68d1afb35c2032c68dbdf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
spec.addAuxFile("681dcbedcf7ca14bb44134abd1d8da3f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
spec.addAuxFile("0f58e7f0909b84897fea5daebd9d2948", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
spec.addAuxFile("2832e48c12b1d8811ccd319a8ffb8dc1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
spec.addAuxFile("a836b92ac17b8ff9788e2aaa9116b5d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
spec.addAuxFile("31f9aa7ddad7809bc2f6675014dd4eaf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
spec.addAuxFile("958667ce6f92106a32a77098c1533d4f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
spec.addAuxFile("5e87db30702e44031920f7417cfac844", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
spec.addAuxFile("b82846df660f0aac8429aec57c2a62d6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
spec.addAuxFile("22fee04ffca7fa489ae2e66309de12e4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
spec.addAuxFile("2de22ad840bf40621e51316728a32fe9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
spec.addAuxFile("6c84a067016c63e8c2face2de800acc7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
spec.addAuxFile("2629883b99428f51e2d90d820b45504a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
spec.addAuxFile("6909d50a7da337cd294828b32b945eb8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
spec.addAuxFile("e0f0d44cb4bc0557ee55b8b2aaa0cb9f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
spec.addAuxFile("d69d08fd37f63941eea52d7b66a625df", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
spec.addAuxFile("de1795f42397d1282c012a3b9c396b5c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
spec.addAuxFile("d53431022f7387fe9ac47814ab1fcd88", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
spec.addAuxFile("f6e52c5659f53afdcfc69c25272b9e99", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
spec.addAuxFile("c2fb3a31d02df03c35afbe7f2284ad66", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("d1b3d08c6e9565a1dab727d089085761", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("c0fadfcfd88cec81ba0d57b33bdec277", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
spec.addAuxFile("a72253b8e06dc6c653355b20e56e2f6e", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("23ca7c647e3e53eb9b713d46b92bf6a2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("cd4ef2d43dc98f1bd7e6db532c60b3d1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
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")
public Object[][] makeMyDataProvider() {
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 20:62,954,114-63,025,520","22471ea4a12e5139aef62bf8ff2a5b63"});
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 20:62,954,114-63,025,520","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 ","977298255b04d66c17bb5466da8251f7"});
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)
} 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)
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 class FragmentUtilsTest extends TestDataProvider {
List<TestState> statesForPileup = new ArrayList<TestState>();
List<TestState> statesForReads = new ArrayList<TestState>();
List<TestState> statesForPileup = new ArrayList<>();
List<TestState> statesForReads = new ArrayList<>();
private FragmentUtilsTest(String name, int readLen, int leftStart, int rightStart,
boolean leftIsFirst, boolean leftIsNegative) {
@ -70,8 +70,8 @@ public class FragmentUtilsUnitTest extends BaseTest {
boolean posCoveredByRight = pos >= right.getAlignmentStart() && pos <= right.getAlignmentEnd();
if ( posCoveredByLeft || posCoveredByRight ) {
List<GATKSAMRecord> reads = new ArrayList<GATKSAMRecord>();
List<Integer> offsets = new ArrayList<Integer>();
List<GATKSAMRecord> reads = new ArrayList<>();
List<Integer> offsets = new ArrayList<>();
if ( posCoveredByLeft ) {
reads.add(left);
@ -174,7 +174,7 @@ public class FragmentUtilsUnitTest extends BaseTest {
@DataProvider(name = "MergeFragmentsTest")
public Object[][] createMergeFragmentsTest() throws Exception {
List<Object[]> tests = new ArrayList<Object[]>();
List<Object[]> tests = new ArrayList<>();
final String leftFlank = "CCC";
final String rightFlank = "AAA";
@ -248,29 +248,29 @@ public class FragmentUtilsUnitTest extends BaseTest {
final byte[] commonQuals = Utils.dupBytes((byte)30, common.length());
final String adapter = "NNNN";
final GATKSAMRecord read1 = makeOverlappingRead(adapter, 30, common, commonQuals, "", 30, 10);
final GATKSAMRecord read2 = makeOverlappingRead("", 30, common, commonQuals, adapter, 30, 10);
final GATKSAMRecord readLeftAdapter = makeOverlappingRead(adapter, 30, common, commonQuals, "", 30, 10);
final GATKSAMRecord readRightAdapter = makeOverlappingRead("", 30, common, commonQuals, adapter, 30, 10);
final GATKSAMRecord expectedMerged = makeOverlappingRead("", 30, common, commonQuals, "", 30, 10);
read1.setCigarString("4S" + common.length() + "M");
read1.setProperPairFlag(true);
read1.setReadPairedFlag(true);
read1.setFirstOfPairFlag(true);
read1.setReadNegativeStrandFlag(true);
read1.setMateNegativeStrandFlag(false);
read1.setMateAlignmentStart(read2.getAlignmentStart());
read2.setCigarString(common.length() + "M4S");
read2.setProperPairFlag(true);
read2.setReadPairedFlag(true);
read2.setFirstOfPairFlag(false);
read2.setReadNegativeStrandFlag(false);
read2.setMateNegativeStrandFlag(true);
read2.setMateAlignmentStart(read1.getAlignmentStart());
readLeftAdapter.setCigarString(adapter.length() + "S" + common.length() + "M");
readLeftAdapter.setProperPairFlag(true);
readLeftAdapter.setReadPairedFlag(true);
readLeftAdapter.setFirstOfPairFlag(true);
readLeftAdapter.setReadNegativeStrandFlag(true);
readLeftAdapter.setMateNegativeStrandFlag(false);
readLeftAdapter.setMateAlignmentStart(readRightAdapter.getAlignmentStart());
readRightAdapter.setCigarString(common.length() + "M4S");
readRightAdapter.setProperPairFlag(true);
readRightAdapter.setReadPairedFlag(true);
readRightAdapter.setFirstOfPairFlag(false);
readRightAdapter.setReadNegativeStrandFlag(false);
readRightAdapter.setMateNegativeStrandFlag(true);
readRightAdapter.setMateAlignmentStart(readLeftAdapter.getAlignmentStart());
final int insertSize = common.length() - 1;
read1.setInferredInsertSize(-insertSize);
read2.setInferredInsertSize(insertSize);
final int insertSize = common.length();
readLeftAdapter.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.getReadBases(), expectedMerged.getReadBases());
Assert.assertEquals(actual.getReadGroup(), expectedMerged.getReadGroup());
@ -282,24 +282,25 @@ public class FragmentUtilsUnitTest extends BaseTest {
@Test(enabled = true)
public void testHardClippingBeforeMergeResultingInCompletelyContainedSecondRead() {
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 read2 = makeOverlappingRead("", 30, Utils.dupString("A", 7), Utils.dupBytes((byte)30, 7), adapter, 30, 10);
read1.setCigarString("4S10M");
read1.setProperPairFlag(true);
read1.setFirstOfPairFlag(true);
read1.setReadNegativeStrandFlag(true);
read1.setMateAlignmentStart(10);
read2.setCigarString("7M4S");
read2.setProperPairFlag(true);
read2.setFirstOfPairFlag(false);
read2.setReadNegativeStrandFlag(false);
final GATKSAMRecord readLeftAdapter = makeOverlappingRead(adapter, 30, Utils.dupString("A", 10), Utils.dupBytes((byte)30, 10), "", 30, 10);
final GATKSAMRecord readRightAdapter = makeOverlappingRead("", 30, Utils.dupString("A", minReadSize), Utils.dupBytes((byte)30, minReadSize), adapter, 30, 10);
readLeftAdapter.setCigarString(adapter.length() + "S10M");
readLeftAdapter.setProperPairFlag(true);
readLeftAdapter.setFirstOfPairFlag(true);
readLeftAdapter.setReadNegativeStrandFlag(true);
readLeftAdapter.setMateAlignmentStart(10);
readRightAdapter.setCigarString(minReadSize + "M4S");
readRightAdapter.setProperPairFlag(true);
readRightAdapter.setFirstOfPairFlag(false);
readRightAdapter.setReadNegativeStrandFlag(false);
final int insertSize = 7 - 1;
read1.setInferredInsertSize(insertSize);
read2.setInferredInsertSize(-insertSize);
final int insertSize = minReadSize;
readLeftAdapter.setInferredInsertSize(insertSize);
readRightAdapter.setInferredInsertSize(-insertSize);
final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(read1, read2);
final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(readLeftAdapter, readRightAdapter);
Assert.assertNull(actual);
}
@ -356,7 +357,7 @@ public class FragmentUtilsUnitTest extends BaseTest {
@DataProvider(name = "AdjustFragmentsTest")
public Object[][] createAdjustFragmentsTest() throws Exception {
List<Object[]> tests = new ArrayList<Object[]>();
List<Object[]> tests = new ArrayList<>();
final String leftFlank = "CCC";
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.setMateNegativeStrandFlag(true);
read.setMateAlignmentStart(start - 1);
read.setInferredInsertSize(goodBases - 1);
read.setInferredInsertSize(goodBases);
tests.add(new Object[]{0, goodBases, nClips, read});
}
}
@ -738,6 +738,6 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest {
}
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.setMateNegativeStrandFlag(true);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, myStart + fragmentSize + 1);
Assert.assertEquals(boundary, myStart + fragmentSize);
// Test case 2: positive strand, second read
read = makeRead(fragmentSize, mateStart);
@ -99,7 +99,7 @@ public class ReadUtilsUnitTest extends BaseTest {
read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, myStart + fragmentSize + 1);
Assert.assertEquals(boundary, myStart + fragmentSize);
// Test case 3: negative strand, second read
read = makeRead(fragmentSize, mateStart);