diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java index 397179f35..9da43df3f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java @@ -63,7 +63,9 @@ import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; import org.broadinstitute.gatk.utils.contexts.AlignmentContext; -import org.broadinstitute.gatk.utils.genotyper.*; +import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.genotyper.SampleListUtils; import org.broadinstitute.gatk.utils.haplotype.Haplotype; import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState; import org.broadinstitute.gatk.utils.pileup.PileupElement; @@ -250,8 +252,9 @@ public class ReferenceConfidenceModel { // as our GLs for the site. final GenotypeLikelihoods leastConfidenceGLs = getGLwithWorstGQ(indelGLs, snpGLs); - gb.GQ((int) (-10 * leastConfidenceGLs.getLog10GQ(GenotypeType.HOM_REF))); - gb.PL(leastConfidenceGLs.getAsPLs()); + final int[] leastConfidenceGLsAsPLs = leastConfidenceGLs.getAsPLs(); + gb.GQ(GATKVariantContextUtils.calculateGQFromPLs(leastConfidenceGLsAsPLs)); + gb.PL(leastConfidenceGLsAsPLs); //gb.attribute(INDEL_INFORMATIVE_DEPTH, nIndelInformativeReads); vcb.genotypes(gb.make()); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java index 18379f990..f0e4ca9eb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java @@ -246,7 +246,7 @@ public class GVCFWriter implements VariantContextWriter { final int[] minPLs = block.getMinPLs(); gb.PL(minPLs); - final int gq = genotypeQualityFromPLs(minPLs); + final int gq = GATKVariantContextUtils.calculateGQFromPLs(minPLs); gb.GQ(gq); gb.DP(block.getMedianDP()); gb.attribute(GATKVCFConstants.MIN_DP_FORMAT_KEY, block.getMinDP()); @@ -257,26 +257,6 @@ public class GVCFWriter implements VariantContextWriter { return vcb.genotypes(gb.make()).make(); } - - private int genotypeQualityFromPLs(final int[] minPLs) { - int first = minPLs[0]; - int second = minPLs[1]; - if (first > second) { - second = first; - first = minPLs[1]; - } - for (int i = 3; i < minPLs.length; i++) { - final int candidate = minPLs[i]; - if (candidate >= second) continue; - if (candidate <= first) { - second = first; - first = candidate; - } else - second = candidate; - } - return second - first; - } - /** * Helper function to create a new HomRefBlock from a variant context and current genotype * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java index fd15a2834..bb8373b20 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java @@ -86,7 +86,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { //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, "8d30370465d74fd549d76dd31adc4c0c"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "119a30fac57a0e5cf1b8164c1059b22c"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "cf5545094ebb264fa8eb879fd848d9ef"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "a6bbc30b82e7864baf64163d55f5aee5"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "2e81881e92061ad4eb29025ffdc129c7"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "2c67bdc08c8784f2114c2039270b9766"}); @@ -105,8 +105,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { // 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, "822856b75c792be81693019bee672c09"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "6ef5ce3fbc943f15c077a0f12ff5bc2e"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "8bb824886fb0e77d0e8317d69f9d1b62"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "ca87b62a070801e4954d72169b88fb9c"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "63ff771eed3e62340c8938b4963d0add"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1122a0b3849f42d1c4a654f93b660e1b"}); @@ -128,10 +128,10 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { // 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, "2f1534d30b51fd8a7861d73091be2336"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "2307bcb9f9e3468375a389720036b7da"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "450906ce3c11860c25b90cf0a56bb1a0"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "3c0346d41a7e57b45b85a920cc04f51f"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ad7855dbf6dda2060aa93a3ee010b3e"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a0be095ed902a8acdb80fb56ca4e8fb4"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "50e628de2a79cd6887af020b713ca3b8"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "8123d8b68b6fa77ef084f292e191622a"}); return tests.toArray(new Object[][]{}); @@ -146,11 +146,11 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { // 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, "7dc7cfd463ecb7ac535c6ba925c46ef0"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "689d4b9cdc21be370c82251e1f7a3c4f"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "0bc1ca3bff07381a344685b048e76ee4"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "9d1724150feccb0a09b6fad522605bb1"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "af0fe243e3b96e59097187cd16ba1597"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "228e1d2ec2e729a5f79c37f3f2557708"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "2fc7020457dde4439b4133c098d9ab9b"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "8a094080fb25bbcd39325dcdd62bcf65"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "f35192d245babba9764128abad669019"}); return tests.toArray(new Object[][]{}); } @@ -293,7 +293,7 @@ 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("d55ccf214fd5095e6d586c1547cb1a7a")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9fc3c68f46e747b730615c0be98cb013")); spec.disableShadowBCF(); executeTest("testNoCallGVCFMissingPLsBugFix", spec); } @@ -326,7 +326,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations() { 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 -G Standard -G AS_Standard --disableDithering", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("1733d15e960ed473f58a2bfc7f686a2e")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("d986868d83057c0ecdf7ba177b8282f3")); spec.disableShadowBCF(); executeTest(" testAlleleSpecificAnnotations", spec); } @@ -335,7 +335,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testASMQMateRankSumAnnotation() { 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 -A AS_MQMateRankSumTest --disableDithering", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("e6e09a82cade24f8121c81c1d43b5d03")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("87723bd4442c7ec25f65a77d6434957a")); spec.disableShadowBCF(); executeTest(" testASMQMateRankSumAnnotation", spec); } @@ -344,7 +344,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testASInsertSizeRankSum() { 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 -G Standard -G AS_Standard --disableDithering -A AS_InsertSizeRankSum", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("33db0c7e64fc963c160f8bb59d983375")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("a63d6912b2f2fab7debee9488fbbd0b0")); spec.disableShadowBCF(); executeTest(" testASInsertSizeRankSum", spec); } @@ -362,7 +362,7 @@ 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("1176028faca6cd397f581f9e60c474a8")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("446604d4398d4c1bad41b9506624ab91")); spec.disableShadowBCF(); executeTest("testHaplotypeCallerMaxNumPLValues", spec); } @@ -379,7 +379,7 @@ 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("19f5398e4013c06b52c0085fe0b3469e")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("a01abc7e0b4a486125967d3a1ebcc33f")); spec.disableShadowBCF(); executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel", spec); // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log @@ -404,7 +404,7 @@ 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("19f5398e4013c06b52c0085fe0b3469e")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("a01abc7e0b4a486125967d3a1ebcc33f")); spec.disableShadowBCF(); executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel", spec); // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log @@ -414,4 +414,14 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { // Set the log level back logger.setLevel(level); } + + //Regression test for https://github.com/broadinstitute/gsa-unstable/issues/1345 + @Test + public void testHaplotypeCallerGVCFBlocks() { + final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L 1:1-1000000 -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d", + b37KGReference, privateTestDir + "gvcf_blocks_test.bam", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("802c53621bd2004d9052a8e81d91df3e")); + spec.disableShadowBCF(); + executeTest("testHaplotypeCallerGVCFBlocks", spec); + } } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java index 407a49570..d67dd6c01 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java @@ -2314,5 +2314,31 @@ public class GATKVariantContextUtils { builder.attribute(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFrequency.toArray()); } } + + /** + * @param plValues array of PL values + * @return the genotype quality corresponding to the PL values + */ + public static int calculateGQFromPLs(final int[] plValues) { + if ( plValues == null ) throw new IllegalArgumentException("Array of PL values cannot be null."); + if ( plValues.length < 2 ) throw new IllegalArgumentException("Array of PL values must contain at least two elements."); + + int first = plValues[0]; + int second = plValues[1]; + if (first > second) { + second = first; + first = plValues[1]; + } + for (int i = 2; i < plValues.length; i++) { + final int candidate = plValues[i]; + if (candidate >= second) continue; + if (candidate <= first) { + second = first; + first = candidate; + } else + second = candidate; + } + return second - first; + } } diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java index f875d2e8f..20ec7da58 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java @@ -1872,5 +1872,34 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest { final Map calledAltAlleles = new LinkedHashMap<>(); GATKVariantContextUtils.updateChromosomeCountsInfo(calledAltAlleles, calledAlleles, null); } + + @DataProvider(name="gqFromPLsData") + public Object[][] gqFromPLsData() { + return new Object[][]{ + {new int[]{0, 15}, 15}, + {new int[]{15, 0}, 15}, + {new int[]{0, 10, 20}, 10}, + {new int[]{20, 10, 0}, 10}, + {new int[]{0, 10, 20, 30, 40}, 10}, + {new int[]{30, 40, 20, 10, 0}, 10}, + {new int[]{-10, 20, 35}, 30}, + {new int[]{35, 40, -10, 15, 20}, 25}, + {new int[]{0, 10, 20, 30, 40, 50, 5}, 5}, + {new int[]{15, 15, 0, 5}, 5}, + {new int[]{15, 15, 0, 25}, 15}, + {new int[]{0, 15, 0, 25}, 0} + }; + } + + @Test(dataProvider = "gqFromPLsData") + public void testCalculateGQFromPLs(final int[] plValues, final int expectedGQ) { + Assert.assertEquals(GATKVariantContextUtils.calculateGQFromPLs(plValues), expectedGQ); + } + + @Test(expectedExceptions = IllegalArgumentException.class) + public void testCalculateGQFromShortPLArray() { + final int[] plValues = new int[]{0}; + GATKVariantContextUtils.calculateGQFromPLs(plValues); + } }