diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 8d29753ee..128322bfc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -262,12 +262,14 @@ public class UnifiedGenotyper extends LocusWalker, Unif if ( UAC.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED ) headerInfo.add(new VCFInfoHeaderLine(UnifiedGenotyperEngine.NUMBER_OF_DISCOVERED_ALLELES_KEY, 1, VCFHeaderLineType.Integer, "Number of alternate alleles discovered (but not necessarily genotyped) at this site")); headerInfo.add(new VCFInfoHeaderLine(VCFConstants.DOWNSAMPLED_KEY, 0, VCFHeaderLineType.Flag, "Were any of the samples downsampled?")); + headerInfo.add(new VCFInfoHeaderLine(VCFConstants.MLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed")); + headerInfo.add(new VCFInfoHeaderLine(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed")); // also, check to see whether comp rods were included if ( dbsnp.dbsnp.isBound() ) headerInfo.add(new VCFInfoHeaderLine(VCFConstants.DBSNP_KEY, 0, VCFHeaderLineType.Flag, "dbSNP Membership")); - // FORMAT and INFO fields + // FORMAT fields headerInfo.addAll(getSupportedHeaderStrings()); // FILTER fields diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index a4b8c546a..0a06e2203 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -296,6 +296,7 @@ public class UnifiedGenotyperEngine { // determine which alternate alleles have AF>0 final List myAlleles = new ArrayList(vc.getAlleles().size()); + final List alleleCountsofMLE = new ArrayList(vc.getAlleles().size()); myAlleles.add(vc.getReference()); for ( int i = 0; i < vc.getAlternateAlleles().size(); i++ ) { final Allele alternateAllele = vc.getAlternateAllele(i); @@ -304,11 +305,12 @@ public class UnifiedGenotyperEngine { if ( indexOfAllele == -1 ) continue; - int indexOfBestAC = AFresult.getAlleleCountsOfMAP()[indexOfAllele-1]; + final int indexOfBestAC = AFresult.getAlleleCountsOfMAP()[indexOfAllele-1]; // if the most likely AC is not 0, then this is a good alternate allele to use if ( indexOfBestAC != 0 ) { myAlleles.add(alternateAllele); + alleleCountsofMLE.add(AFresult.getAlleleCountsOfMLE()[indexOfAllele-1]); bestGuessIsRef = false; } // if in GENOTYPE_GIVEN_ALLELES mode, we still want to allow the use of a poor allele @@ -355,6 +357,7 @@ public class UnifiedGenotyperEngine { // create the genotypes final GenotypesContext genotypes = afcm.get().subsetAlleles(vc, myAlleles, true,ploidy); + builder.genotypes(genotypes); // print out stats if we have a writer if ( verboseWriter != null && !limitedContext ) @@ -370,6 +373,16 @@ public class UnifiedGenotyperEngine { if ( UAC.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED ) attributes.put(NUMBER_OF_DISCOVERED_ALLELES_KEY, vc.getAlternateAlleles().size()); + // add the MLE AC and AF annotations + if ( alleleCountsofMLE.size() > 0 ) { + attributes.put(VCFConstants.MLE_ALLELE_COUNT_KEY, alleleCountsofMLE); + final double AN = (double)builder.make().getCalledChrCount(); + final ArrayList MLEfrequencies = new ArrayList(alleleCountsofMLE.size()); + for ( int AC : alleleCountsofMLE ) + MLEfrequencies.add((double)AC / AN); + attributes.put(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, MLEfrequencies); + } + if ( !UAC.NO_SLOD && !limitedContext && !bestGuessIsRef ) { //final boolean DEBUG_SLOD = false; @@ -413,7 +426,6 @@ public class UnifiedGenotyperEngine { } // finish constructing the resulting VC - builder.genotypes(genotypes); builder.attributes(attributes); VariantContext vcCall = builder.make(); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java index 87e5efcef..108630607 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java @@ -33,7 +33,9 @@ public final class VCFConstants { // reserved INFO/FORMAT field keys public static final String ANCESTRAL_ALLELE_KEY = "AA"; public static final String ALLELE_COUNT_KEY = "AC"; + public static final String MLE_ALLELE_COUNT_KEY = "MLEAC"; public static final String ALLELE_FREQUENCY_KEY = "AF"; + public static final String MLE_ALLELE_FREQUENCY_KEY = "MLEAF"; public static final String ALLELE_NUMBER_KEY = "AN"; public static final String RMS_BASE_QUALITY_KEY = "BQ"; public static final String CIGAR_KEY = "CIGAR"; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index f2b5075c6..16446a044 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -8,7 +8,6 @@ import org.testng.annotations.Test; import java.io.File; import java.util.Arrays; import java.util.List; -import java.util.Map; // ********************************************************************************** // // Note that this class also serves as an integration test for the VariantAnnotator! // @@ -29,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1, - Arrays.asList("b6c677b2375541fd2db775d0029571e6")); + Arrays.asList("1c6ea045819b151bcd9d98947c5d4c4d")); executeTest("test MultiSample Pilot1", spec); } @@ -37,7 +36,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testWithAllelesPassedIn1() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("3400dfae6db8ed7e1351b1aa52341714")); + Arrays.asList("c09dfbfc5b76acacb616730eaa83a150")); executeTest("test MultiSample Pilot2 with alleles passed in", spec1); } @@ -45,7 +44,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testWithAllelesPassedIn2() { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("0bb67b07ee5315d0486f3a0045a03757")); + Arrays.asList("c51d037e0b1cd0ed3a1cd6c6b29646cf")); executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2); } @@ -53,7 +52,7 @@ public class UnifiedGenotyperIntegrationTest 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("5c5bf3d2676e1a26d521f1f902f73526")); + Arrays.asList("0a085eac119c91d63fdd4a7e9a5e45af")); executeTest("test SingleSample Pilot2", spec); } @@ -61,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultipleSNPAlleles() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + testDir + "multiallelic.snps.bam -o %s -L " + testDir + "multiallelic.snps.intervals", 1, - Arrays.asList("eb6c8b7680f40b5fdac6e451c623ab81")); + Arrays.asList("bdbb67743c9f75ac60d0a10f94856361")); executeTest("test Multiple SNP alleles", spec); } @@ -69,7 +68,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testBadRead() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH -I " + testDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1, - Arrays.asList("e2cf97bca4a720ca64ca7f682da6c9f0")); + Arrays.asList("bf60763a6e9c9d3987cfbac43b941a48")); executeTest("test bad read", spec); } @@ -77,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testReverseTrim() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1, - Arrays.asList("0c195201574815559757885c693b6640")); + Arrays.asList("1e991a6a7288be7ac603ef6467fb1ac2")); executeTest("test reverse trim", spec); } @@ -87,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - private final static String COMPRESSED_OUTPUT_MD5 = "6209a19a33ac9e187a9074cee549f93b"; + private final static String COMPRESSED_OUTPUT_MD5 = "3136826ec99366b0285b278aba35cec1"; @Test public void testCompressedOutput() { @@ -108,7 +107,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // Note that we need to turn off any randomization for this to work, so no downsampling and no annotations - String md5 = "34cb7146c037925e8f324cffd986834d"; + String md5 = "7824468b8290ffb7795a1ec3e493c1a4"; WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1, @@ -140,7 +139,7 @@ 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("f48e4898c741c84354da3a0562cb44e1")); + Arrays.asList("86121f5094f26c8b2e320c1f5dea4ae3")); executeTest("test min_base_quality_score 26", spec); } @@ -148,7 +147,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testSLOD() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("f4ef85f1ed72e35b91b0469edf5956ad")); + Arrays.asList("fe4a96f0049edd466c030def4c62a224")); executeTest("test SLOD", spec); } @@ -156,7 +155,7 @@ 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("ea219bdce9596e8649ad1d39e24e333a")); + Arrays.asList("ca8d0d91fd0cef93d4a606dec84a7986")); executeTest("test NDA", spec); } @@ -164,23 +163,23 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testCompTrack() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("9d5c51379e1b1031da5735aa8c965766")); + Arrays.asList("7c3518d356c05c6b9a8918357c260bfe")); executeTest("test using comp track", spec); } @Test public void testOutputParameterSitesOnly() { - testOutputParameters("-sites_only", "ac8bea16be247d9e39d66a6305409f57"); + testOutputParameters("-sites_only", "fe204cef499e5aceb2732ba2e45903ad"); } @Test public void testOutputParameterAllConfident() { - testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "1e908a3164adbab10dcb6415e2645954"); + testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "1ab8b68891d1531923a40d594250e8e0"); } @Test public void testOutputParameterAllSites() { - testOutputParameters("--output_mode EMIT_ALL_SITES", "eee23523912b51b249472e6d5fc0aece"); + testOutputParameters("--output_mode EMIT_ALL_SITES", "ab179ef6ece3ab9e6b1ff5800cb89ebd"); } private void testOutputParameters(final String args, final String md5) { @@ -194,7 +193,7 @@ 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("355bee3d375e994e4a3b07f7a8d267a0")); + Arrays.asList("a19c6195211b0ff036c746c7e11490ed")); executeTest("test confidence 1", spec1); } @@ -202,7 +201,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testConfidence2() { WalkerTest.WalkerTestSpec spec2 = 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_emit_conf 10 ", 1, - Arrays.asList("72d9ea93591b17535b7f5b53e1d064cb")); + Arrays.asList("3fc3c36edaac133b4c11b20a5af915c4")); executeTest("test confidence 2", spec2); } @@ -213,12 +212,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // -------------------------------------------------------------------------------------------------------------- @Test public void testHeterozyosity1() { - testHeterozosity( 0.01, "0ffd19f90b05652e45f58e4a959ae304" ); + testHeterozosity( 0.01, "82caf6c25d3aeabf7978016474e04fd0" ); } @Test public void testHeterozyosity2() { - testHeterozosity( 1.0 / 1850, "b6dbfb567e433273fe90b0d038556a9f" ); + testHeterozosity( 1.0 / 1850, "d2a7ba1fa2d1a4153f685f3b3f6d55a2" ); } private void testHeterozosity(final double arg, final String md5) { @@ -242,7 +241,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("c9675bc1ca6c82cb60d39d9395881c96")); + Arrays.asList("b574087efc5b259f69c429f1f415da0a")); executeTest(String.format("test multiple technologies"), spec); } @@ -261,7 +260,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("6e4089986d08d46a8d0b4ddfd611a7c3")); + Arrays.asList("1b9556725b6a2cb52ad6745e9eca37e6")); executeTest(String.format("test calling with BAQ"), spec); } @@ -280,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("80a5a499cc553ee579ba93dcb967e5ef")); + Arrays.asList("9388a1216957c4722fe54af06a05f242")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -295,7 +294,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -minIndelCnt 1" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("9271105e630ab39cf1c88b338da54594")); + Arrays.asList("8f942000baaf522fcea29691fe5ef75d")); executeTest(String.format("test indel caller in SLX with low min allele count"), spec); } @@ -308,7 +307,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("d77a379429ca848cea552c4697b86472")); + Arrays.asList("4b8822ccc9ac04bee37bf0c9922108f9")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -318,7 +317,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("f83c4f370ed0a343ca0808e5da3d997d")); + Arrays.asList("13160041d8ebfb2080981f89e39eeb4f")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec); } @@ -328,7 +327,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("ca5459e93a9955aec8f93abf7f84e5ed")); + Arrays.asList("59e874d76e42eafd98ad961eb70706bc")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec); } @@ -336,13 +335,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSampleIndels1() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1, - Arrays.asList("04aaeff1e9f97bbf2dc2d6d754f25a0d")); + Arrays.asList("eaef9cc984a95b5ccb4c4c1f7c20c235")); List result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst(); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1, - Arrays.asList("5c7db047ae9417d37c6bbda1d8ea6019")); + Arrays.asList("b4df2bf0d820c6fc11fabcafe18bb769")); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); } @@ -352,7 +351,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + testDir + vcf + " -I " + validationDataLocation + "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1, - Arrays.asList("3e3ac23846801c34acbf10a1a527264a")); + Arrays.asList("95226301a014347efc90e5f750a0db60")); executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec); } @@ -385,7 +384,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinIndelFraction0() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.0", 1, - Arrays.asList("90e8140f114e026f2a0e7a881baa3f20")); + Arrays.asList("a3ea0eea74f2031ebb2ea0edfa14c945")); executeTest("test minIndelFraction 0.0", spec); } @@ -393,7 +392,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinIndelFraction25() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.25", 1, - Arrays.asList("db70b7a015fa882c8ce1e4c43f589f22")); + Arrays.asList("a3741b9de95e5858640220d62a0d318c")); executeTest("test minIndelFraction 0.25", spec); } @@ -401,7 +400,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinIndelFraction100() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 1", 1, - Arrays.asList("50a6774b7d8f71fe0e125c204d50ba84")); + Arrays.asList("c1911f6ede7b4e8e83209ead66329596")); executeTest("test minIndelFraction 1.0", spec); } }