From f0bd1b5ae5a4c8fb1eb0385425a235c41db8f26a Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 8 Jan 2013 15:46:32 -0500 Subject: [PATCH] Okay, all public->protected dependencies are gone except for the BQSR arguments. I'll need to think through this but should be able to make that work too. --- .../gatk/arguments/StandardCallerArgumentCollection.java | 0 .../genotyper/SNPGenotypeLikelihoodsCalculationModel.java | 1 + .../sting/gatk/examples/GATKPaperGenotyper.java | 8 +++++--- .../sting/utils}/genotyper/DiploidGenotype.java | 2 +- .../sting/utils/recalibration/BQSRMode.java | 0 .../sting/utils/recalibration/EventType.java | 0 6 files changed, 7 insertions(+), 4 deletions(-) rename {public => protected}/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java (100%) rename {protected/java/src/org/broadinstitute/sting/gatk/walkers => public/java/src/org/broadinstitute/sting/utils}/genotyper/DiploidGenotype.java (98%) rename {protected => public}/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java (100%) rename {protected => public}/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java (100%) diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java rename to protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index 80a787fe0..4cc152d53 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -37,6 +37,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.DiploidGenotype; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java index 6482354a9..1c227170d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java @@ -33,8 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; -import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype; +import org.broadinstitute.sting.utils.genotyper.DiploidGenotype; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -50,6 +49,9 @@ import java.io.PrintStream; */ @DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) public class GATKPaperGenotyper extends LocusWalker implements TreeReducible { + + public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3; + // the possible diploid genotype strings private static enum GENOTYPE { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT } @@ -73,7 +75,7 @@ public class GATKPaperGenotyper extends LocusWalker implements Tre ReadBackedPileup pileup = context.getBasePileup().getPileupWithoutMappingQualityZeroReads(); double likelihoods[] = getReferencePolarizedPriors(ref.getBase(), - UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY, + HUMAN_SNP_HETEROZYGOSITY, 0.01); // get the bases and qualities from the pileup byte bases[] = pileup.getBases(); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java similarity index 98% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java rename to public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java index 86047d30b..6d90038d7 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.genotyper; +package org.broadinstitute.sting.utils.genotyper; import org.broadinstitute.variant.utils.BaseUtils; diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java similarity index 100% rename from protected/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java