diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index fb7fb652c..f3f54060f 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -459,7 +459,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In // the minimum length of a read we'd consider using for genotyping private final static int MIN_READ_LENGTH = 10; - private List samplesList = new ArrayList(); + private List samplesList = new ArrayList<>(); private final static Allele FAKE_REF_ALLELE = Allele.create("N", true); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file private final static Allele FAKE_ALT_ALLELE = Allele.create("", false); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java index 073d54ec5..8394baa72 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java @@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleComplex1() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "d21f15a5809fe5259af41ae6774af6f1"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "e7b28ea087e8624f1e596c9d65381fea"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { @@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleGGAComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538", - "d4a0797c2fd4c103bf9a137633376156"); + "321dc9f3d330790bac7981ffae00cb0c"); } @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "a9872228d0275a30f5a1f7e070a9c9f4"); + "2a72a9b5c6778b99bf155a7c5e90d11e"); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index dbdd0afcd..f9bab8ea7 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -78,12 +78,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "e9167a1bfc0fc276586788d1ce1be408"); + HCTest(CEUTRIO_BAM, "", "f25b9cfc85995cbe8eb6ba5a126d713d"); } @Test public void testHaplotypeCallerSingleSample() { - HCTest(NA12878_BAM, "", "b1d46afb9659ac3b92a3d131b58924ef"); + HCTest(NA12878_BAM, "", "19d685727ec60b3568f313bc44f79b49"); } @Test(enabled = false) // can't annotate the rsID's yet @@ -94,7 +94,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSampleGGA() { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", - "d83856b8136776bd731a8037c16b71fa"); + "6da65f1d396b9c709eb6246cf3f615c1"); } @Test @@ -110,7 +110,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleIndelQualityScores() { - HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "70c4476816f5d35c9978c378dbeac09b"); + HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "e3db7d56154e36eeb887259bea4b241d"); } private void HCTestNearbySmallIntervals(String bam, String args, String md5) { @@ -147,7 +147,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerNearbySmallIntervals() { - HCTestNearbySmallIntervals(NA12878_BAM, "", "947aae309ecab7cd3f17ff9810884924"); + HCTestNearbySmallIntervals(NA12878_BAM, "", "6e170d03047caefc2fba3f1c1f8de132"); } // This problem bam came from a user on the forum and it spotted a problem where the ReadClipper @@ -186,7 +186,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestReducedBam() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1, - Arrays.asList("0124c4923d96ec0f8222b596dd4ef534")); + Arrays.asList("40416433baf96f4e84a058459717060b")); executeTest("HC calling on a ReducedRead BAM", spec); } @@ -194,7 +194,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void testReducedBamWithReadsNotFullySpanningDeletion() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1, - Arrays.asList("0e020dcfdf249225714f5cd86ed3869f")); + Arrays.asList("cf1461ce829023ea9920fbfeb534eb97")); executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec); } @@ -208,7 +208,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestDBSNPAnnotationWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1, - Arrays.asList("446a786bb539f3ec2084dd75167568aa")); + Arrays.asList("45ca324be3917655e645d6c290c9280f")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -217,7 +217,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering -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("9587029b702bb59bd4dfec69eac4c210")); + Arrays.asList("b7037770b7953cdf858764b99fa243ed")); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java index 62e685eab..857d0fc9e 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java @@ -61,7 +61,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest { List tests = new ArrayList(); for ( final int nct : Arrays.asList(1, 2, 4) ) { - tests.add(new Object[]{nct, "ef42a438b82681d1c0f921c57e16ff12"}); + tests.add(new Object[]{nct, "bd2a57e6b0cffb4cbdba609a6c1683dc"}); } return tests.toArray(new Object[][]{}); diff --git a/protected/java/test/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java index 9530ea41f..651beffc8 100644 --- a/protected/java/test/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java @@ -233,7 +233,7 @@ public class PerReadAlleleLikelihoodMapUnitTest extends BaseTest { tests.add(new Object[]{100, 0.01, true, Arrays.asList(-5.0, -10.0)}); tests.add(new Object[]{100, 0.01, false, Arrays.asList(-5.0, -10.0, -3.0)}); tests.add(new Object[]{100, 0.01, false, Arrays.asList(-5.0, -10.0, -2.0)}); - tests.add(new Object[]{100, 0.01, true, Arrays.asList(-5.0, -10.0, -4.0)}); + tests.add(new Object[]{100, 0.01, true, Arrays.asList(-5.0, -10.0, -4.2)}); tests.add(new Object[]{100, 0.001, true, Arrays.asList(-5.0, -10.0)}); tests.add(new Object[]{100, 0.001, false, Arrays.asList(-5.0, -10.0, 0.0)}); @@ -243,7 +243,7 @@ public class PerReadAlleleLikelihoodMapUnitTest extends BaseTest { @Test(dataProvider = "PoorlyModelledReadData") public void testPoorlyModelledRead(final int readLen, final double maxErrorRatePerBase, final boolean expected, final List log10likelihoods) { final byte[] bases = Utils.dupBytes((byte)'A', readLen); - final byte[] quals = Utils.dupBytes((byte) 30, readLen); + final byte[] quals = Utils.dupBytes((byte) 40, readLen); final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, readLen + "M"); @@ -279,7 +279,7 @@ public class PerReadAlleleLikelihoodMapUnitTest extends BaseTest { final double likelihood = bad ? -100.0 : 0.0; final byte[] bases = Utils.dupBytes((byte)'A', readLen); - final byte[] quals = Utils.dupBytes((byte) 30, readLen); + final byte[] quals = Utils.dupBytes((byte) 40, readLen); final Allele allele = Allele.create(Utils.dupString("A", readI+1)); diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java index 8067d67bc..70be85f54 100644 --- a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java +++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java @@ -321,7 +321,7 @@ public class PerReadAlleleLikelihoodMap { * @return the list of reads removed from this map because they are poorly modelled */ public List filterPoorlyModelledReads(final double maxErrorRatePerBase) { - final List removedReads = new LinkedList(); + final List removedReads = new LinkedList<>(); final Iterator>> it = likelihoodReadMap.entrySet().iterator(); while ( it.hasNext() ) { final Map.Entry> record = it.next(); @@ -356,8 +356,8 @@ public class PerReadAlleleLikelihoodMap { * @return true if none of the log10 likelihoods imply that the read truly originated from one of the haplotypes */ protected boolean readIsPoorlyModelled(final GATKSAMRecord read, final Collection log10Likelihoods, final double maxErrorRatePerBase) { - final double maxErrorsForRead = Math.ceil(read.getReadLength() * maxErrorRatePerBase); - final double log10QualPerBase = -3.0; + final double maxErrorsForRead = Math.min(2.0, Math.ceil(read.getReadLength() * maxErrorRatePerBase)); + final double log10QualPerBase = -4.0; final double log10MaxLikelihoodForTrueAllele = maxErrorsForRead * log10QualPerBase; for ( final double log10Likelihood : log10Likelihoods )