From 5b6d279a2e6ebe1c20dab124561307da890408a8 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Wed, 29 Jun 2011 10:21:27 -0400 Subject: [PATCH 1/4] Two bug fixes: a) Modified the way clipped bases are dealt with in ReadPosRankSumTest when annotating indels. Cigar string cannot be trusted because BWA can clip good high quality bases and some sites get incorrect ReadPos annotations if BWA systematically clips at an indel breakpoint. b) PL header needs to specify "." as length. Otherwise we fail VCF validation if multiallelic sites are present. --- .../walkers/annotator/ReadPosRankSumTest.java | 85 ++++++++++++++++++- .../indels/PairHMMIndelErrorModel.java | 8 +- .../sting/utils/codecs/vcf/VCFUtils.java | 2 +- 3 files changed, 86 insertions(+), 9 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index 2a17cd436..727904a3b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java @@ -4,9 +4,11 @@ import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; +import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.AlignmentUtils; +import net.sf.samtools.*; import java.util.Arrays; import java.util.HashMap; @@ -67,20 +69,95 @@ public class ReadPosRankSumTest extends RankSumTest { altLikelihood = like; } } - int readPos = AlignmentUtils.calcAlignmentByteArrayOffset(p.getRead().getCigar(), p.getOffset(), 0, 0); - final int numAlignedBases = AlignmentUtils.getNumAlignedBases(p.getRead()); + + int readPos = getOffsetFromClippedReadStart(p.getRead(), p.getOffset()); + final int numAlignedBases = getNumAlignedBases(p.getRead()); + + int rp = readPos; if( readPos > numAlignedBases / 2 ) { readPos = numAlignedBases - ( readPos + 1 ); } + //if (DEBUG) System.out.format("R:%s start:%d C:%s offset:%d rp:%d readPos:%d alignedB:%d\n",p.getRead().getReadName(),p.getRead().getAlignmentStart(),p.getRead().getCigarString(),p.getOffset(), rp, readPos, numAlignedBases); - if (refLikelihood > (altLikelihood + INDEL_LIKELIHOOD_THRESH)) + + // if event is beyond span of read just return and don't consider this element. This can happen, for example, with reads + // where soft clipping still left strings of low quality bases but these are later removed by indel-specific clipping. + // if (readPos < -1) + // return; + if (refLikelihood > (altLikelihood + INDEL_LIKELIHOOD_THRESH)) { refQuals.add((double)readPos); - else if (altLikelihood > (refLikelihood + INDEL_LIKELIHOOD_THRESH)) + //if (DEBUG) System.out.format("REF like: %4.1f, pos: %d\n",refLikelihood,readPos); + } + else if (altLikelihood > (refLikelihood + INDEL_LIKELIHOOD_THRESH)) { altQuals.add((double)readPos); + //if (DEBUG) System.out.format("ALT like: %4.1f, pos: %d\n",refLikelihood,readPos); + + } } } } + int getNumClippedBasesAtStart(SAMRecord read) { + // compute total number of clipped bases (soft or hard clipped) + // check for hard clips (never consider these bases): + final Cigar c = read.getCigar(); + final CigarElement first = c.getCigarElement(0); + + int numStartClippedBases = 0; + if (first.getOperator() == CigarOperator.H) { + numStartClippedBases = first.getLength(); + } + byte[] unclippedReadBases = read.getReadBases(); + byte[] unclippedReadQuals = read.getBaseQualities(); + + // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative, + // and may leave a string of Q2 bases still hanging off the reads. + for (int i=numStartClippedBases; i < unclippedReadBases.length; i++) { + if (unclippedReadQuals[i] < PairHMMIndelErrorModel.BASE_QUAL_THRESHOLD) + numStartClippedBases++; + else + break; + + } + + return numStartClippedBases; + } + + int getNumAlignedBases(SAMRecord read) { + return read.getReadLength() - getNumClippedBasesAtStart(read) - getNumClippedBasesAtEnd(read); + } + + int getNumClippedBasesAtEnd(SAMRecord read) { + // compute total number of clipped bases (soft or hard clipped) + // check for hard clips (never consider these bases): + final Cigar c = read.getCigar(); + CigarElement last = c.getCigarElement(c.numCigarElements()-1); + + int numEndClippedBases = 0; + if (last.getOperator() == CigarOperator.H) { + numEndClippedBases = last.getLength(); + } + byte[] unclippedReadBases = read.getReadBases(); + byte[] unclippedReadQuals = read.getBaseQualities(); + + // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative, + // and may leave a string of Q2 bases still hanging off the reads. + for (int i=unclippedReadBases.length-numEndClippedBases-1; i >= 0; i-- ){ + if (unclippedReadQuals[i] < PairHMMIndelErrorModel.BASE_QUAL_THRESHOLD) + numEndClippedBases++; + else + break; + } + + + return numEndClippedBases; + } + + int getOffsetFromClippedReadStart(SAMRecord read, int offset) { + + + return offset - getNumClippedBasesAtStart(read); + } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index e7b9cfa68..ab7ae4184 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -32,9 +32,9 @@ import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; /*import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate; -import org.broadinstitute.sting.walkers.IndelCountCovariates.RecalDataManager; -import org.broadinstitute.sting.walkers.IndelCountCovariates.RecalDatum; -import org.broadinstitute.sting.walkers.IndelCountCovariates.RecalibrationArgumentCollection; +import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager; +import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDatum; +import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalibrationArgumentCollection; */import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.classloader.PluginManager; @@ -57,7 +57,7 @@ import java.util.regex.Pattern; public class PairHMMIndelErrorModel { - private final int BASE_QUAL_THRESHOLD = 10; + public static final int BASE_QUAL_THRESHOLD = 20; private static final int MATCH_OFFSET = 0; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java index e919d5c25..ecede068e 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java @@ -190,7 +190,7 @@ public class VCFUtils { result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype")); result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality")); result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)")); - result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic")); + result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, -1, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; if site is not biallelic, number of likelihoods if n*(n+1)/2")); return result; } From f736a1d61b859f5c439cfcb856faa3a88011ae82 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Wed, 29 Jun 2011 13:37:15 -0400 Subject: [PATCH 2/4] Updated md5's from previous checkin --- .../UnifiedGenotyperIntegrationTest.java | 48 +++++++++---------- .../BatchMergeIntegrationTest.java | 2 +- 2 files changed, 25 insertions(+), 25 deletions(-) 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 51f2b5786..20fa7719f 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 @@ -28,7 +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("a604a64252a8538b7d13f52bd068f797")); + Arrays.asList("258e1954e6ae55c89abc6a716e19cbe0")); executeTest("test MultiSample Pilot1", spec); } @@ -54,12 +54,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testWithAllelesPassedIn() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("5844eda3596732a16c8559f5bfbe1723")); + Arrays.asList("edeb1db288a24baff59575ceedd94243")); executeTest("test MultiSample Pilot2 with alleles passed in", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("db4664a1785c4efb4cd9057478aa846f")); + Arrays.asList("581990130d90071b084024f4cd7caf91")); executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2); } @@ -67,7 +67,7 @@ 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("36c70ec27a25f88fe2364bba2f961843")); + Arrays.asList("d120db27d694a6da32367cc4fb5770fa")); executeTest("test SingleSample Pilot2", spec); } @@ -77,7 +77,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - private final static String COMPRESSED_OUTPUT_MD5 = "212eab2024903997625ba98009063226"; + private final static String COMPRESSED_OUTPUT_MD5 = "75e5c430ed39f79f24e375037a388dc4"; @Test public void testCompressedOutput() { @@ -107,7 +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 = "f83a33a1ecc350cae0c002e4a43a7861"; + String md5 = "a29615dd37222a11b8dadd341b53e43c"; 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, @@ -138,9 +138,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testCallingParameters() { HashMap e = new HashMap(); - e.put( "--min_base_quality_score 26", "d10d0be159d80e22b9c81970ee098daf" ); - e.put( "--min_mapping_quality_score 26", "f76099c403b60b6045a0ae7d9f589dc4" ); - e.put( "--p_nonref_model GRID_SEARCH", "cda395fdf7352e07537610f52a6d0cdc" ); + e.put( "--min_base_quality_score 26", "93e6269e38db9bc1732555e9969e3648" ); + e.put( "--min_mapping_quality_score 26", "64be99183c100caed4aa5f8bad64c7e9" ); + e.put( "--p_nonref_model GRID_SEARCH", "0592fe33f705ad8e2f13619fcf157805" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -153,9 +153,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOutputParameter() { HashMap e = new HashMap(); - e.put( "-sites_only", "9b85d9c10d634315d20aefa565dbab60" ); - e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "245abbb39de43e89f63918a6771c0c14" ); - e.put( "--output_mode EMIT_ALL_SITES", "fb7a59b318ecdb46fd96024be7e41e0e" ); + e.put( "-sites_only", "1483e637dc0279935a7f90d136d147bb" ); + e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "adcd91bc7dae8020df8caf1a30060e98" ); + e.put( "--output_mode EMIT_ALL_SITES", "b708acc2fa40f336bcd2d0c70091e07e" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -169,12 +169,12 @@ 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("f76099c403b60b6045a0ae7d9f589dc4")); + Arrays.asList("64be99183c100caed4aa5f8bad64c7e9")); executeTest("test confidence 1", spec1); 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("879e5ab09bd0d37e0300dd34ec09db81")); + Arrays.asList("e76ca54232d02f0d92730e1affeb804e")); executeTest("test confidence 2", spec2); } @@ -186,8 +186,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testHeterozyosity() { HashMap e = new HashMap(); - e.put( 0.01, "c7123f7b84b402f4959db950326afc13" ); - e.put( 1.0 / 1850, "75e6043a68265ab6deb284bb753801f9" ); + e.put( 0.01, "18d37f7f107853b5e32c757b4e143205" ); + e.put( 1.0 / 1850, "2bcb90ce2f7542bf590f7612018fae8e" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -211,7 +211,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("3f45b2af75123e48b89fa1759c444ec0")); + Arrays.asList("825f05b31b5bb7e82231a15c7e4e2b0d")); executeTest(String.format("test multiple technologies"), spec); } @@ -230,7 +230,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("cede928592575e617f1323866348c256")); + Arrays.asList("0919ab7e513c377610e23a67d33608fa")); executeTest(String.format("test calling with BAQ"), spec); } @@ -244,7 +244,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq OFF", 1, - Arrays.asList("3f45b2af75123e48b89fa1759c444ec0")); + Arrays.asList("825f05b31b5bb7e82231a15c7e4e2b0d")); executeTest(String.format("test calling with BAQ OFF"), spec); } @@ -263,7 +263,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("7fe14d81f12d5d57e3a522b2a4f07fc6")); + Arrays.asList("cb37348c41b8181be829912730f747e1")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -278,7 +278,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -minIndelCnt 1" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("a7da8acce1957334619f3dfeac3d1379")); + Arrays.asList("ca5b6a5fb53ae401b146cc3044f454f2")); executeTest(String.format("test indel caller in SLX witn low min allele count"), spec); } @@ -291,7 +291,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("234b6c336890cc6d9a495bc40f09d126")); + Arrays.asList("ca4343a4ab6d3cce94ce61d7d1910f81")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -301,14 +301,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("9e342e3b73ae4887620195417e1af44a")); + Arrays.asList("3f555b53e9dd14cf7cdf96c24e322364")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("f265726403ca3f28518cb4290b7bee84")); + Arrays.asList("1b9764b783acf7822edc58e6822eef5b")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java index 11eb615d2..7e1d86105 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java @@ -40,7 +40,7 @@ public class BatchMergeIntegrationTest extends WalkerTest { + " -B:alleles,VCF " + alleles + " -I " + bam, 1, - Arrays.asList("b7839064dc4979400af4792460d9884b")); + Arrays.asList("f4ed8f4ef2cba96823c06e90e9d0de35")); executeTest("testBatchMerge UG genotype given alleles:" + new File(bam).getName() + " with " + new File(alleles).getName(), spec); } } \ No newline at end of file From 8586c86bc4d9c02c315100d2278f56e082134875 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 29 Jun 2011 13:56:37 -0400 Subject: [PATCH 3/4] My commit from last week to fix the old dbsnp rod conversion only worked for locus traversals. Updated now to work for all traversals. --- .../sting/gatk/refdata/VariantContextAdaptors.java | 4 ++-- .../variantcontext/VariantContextIntegrationTest.java | 8 ++++---- .../walkers/indels/IndelRealignerIntegrationTest.java | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index 7d7a9d32c..c7c0468e7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -127,9 +127,9 @@ public class VariantContextAdaptors { Map attributes = new HashMap(); attributes.put(VariantContext.ID_KEY, dbsnp.getRsID()); if ( DbSNPHelper.isDeletion(dbsnp) ) { - int index = ref.getLocus().getStart() - ref.getWindow().getStart() - 1; + int index = dbsnp.getStart() - ref.getWindow().getStart() - 1; if ( index < 0 ) - throw new ReviewedStingException("DbSNP conversion requested using a reference context with no window; we will fail to convert deletions"); + return null; // we weren't given enough reference context to create the VariantContext attributes.put(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY, new Byte(ref.getBases()[index])); } Collection genotypes = null; diff --git a/public/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java index 5506b2d27..a72cf0713 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java @@ -19,12 +19,12 @@ public class VariantContextIntegrationTest extends WalkerTest { static HashMap expectations = new HashMap(); static { - expectations.put("-L 1:1-10000 --printPerLocus", "493bf9bcde93c08c8c46f72c8e98cf2f"); - expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "bd9e062b23c2c48fef8c299dc1d294d5"); + expectations.put("-L 1:1-10000 --printPerLocus", "e4ee2eaa3114888e918a1c82df7a027a"); + expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "5b5635e4877d82e8a27d70dac24bda2f"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "ceced3f270b4fe407ee83bc9028becde"); expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "9a9b9e283553c28bf58de1cafa38fe92"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "2097e32988d603d3b353b50218c86d3b"); - expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "91c6a9489256d9ce77c8fedf7221a961"); + expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "033bd952fca048fe1a4f6422b57ab2ed"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "5e40980c02797f90821317874426a87a"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "e5a00766f8c1ff9cf92310bafdec3126"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType NO_VARIATION", "39335acdb34c8a2af433dc50d619bcbc"); @@ -58,7 +58,7 @@ public class VariantContextIntegrationTest extends WalkerTest { // this really just tests that we are seeing the same number of objects over all of chr1 WalkerTestSpec spec = new WalkerTestSpec( root + " -L 1" + " -o %s", 1, // just one output file - Arrays.asList("d2a3f2fe329a0a64145cfd19fde45b99")); + Arrays.asList("529f936aa6c303658b23caf4e527782f")); executeTest("testLargeScaleConversion", spec); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index 0c841d746..2676f7067 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -52,7 +52,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { WalkerTestSpec spec2 = new WalkerTestSpec( baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -D " + GATKDataLocation + "dbsnp_129_b36.rod", 1, - Arrays.asList("78850024ac9ff3ba51b6f097c7041c1d")); + Arrays.asList("05a114623c126b0398fbc1703437461e")); executeTest("realigner known indels only from dbsnp", spec2); } From 9a22d78e4860d1f3aec718e175ef6acec5be1c9e Mon Sep 17 00:00:00 2001 From: Matt Hanna Date: Wed, 29 Jun 2011 14:48:10 -0400 Subject: [PATCH 4/4] Fix up gsalib target to work with new public/private directory structure. --- build.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.xml b/build.xml index 3173cb82d..cf8623bed 100644 --- a/build.xml +++ b/build.xml @@ -978,7 +978,7 @@ - +