From d840a47b117f6be33c632fb8136aa18ca38f83e1 Mon Sep 17 00:00:00 2001 From: depristo Date: Mon, 3 Aug 2009 19:17:15 +0000 Subject: [PATCH] Slight reorganization of genotype interface git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1366 348d0f76-0448-11de-a6fe-93d51630548a --- .../genotyper}/GenotypeLikelihoods.java | 0 .../walkers/genotyper}/SSGGenotypeCall.java | 0 .../genotyper}/SingleSampleGenotyper.java | 0 .../genotype/{calls => }/GenotypeCall.java | 0 .../utils/genotype/GenotypeGenerator.java | 26 ------------------- 5 files changed, 26 deletions(-) rename java/src/org/broadinstitute/sting/{playground/utils => gatk/walkers/genotyper}/GenotypeLikelihoods.java (100%) rename java/src/org/broadinstitute/sting/{utils/genotype/calls => gatk/walkers/genotyper}/SSGGenotypeCall.java (100%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers => gatk/walkers/genotyper}/SingleSampleGenotyper.java (100%) rename java/src/org/broadinstitute/sting/utils/genotype/{calls => }/GenotypeCall.java (100%) delete mode 100644 java/src/org/broadinstitute/sting/utils/genotype/GenotypeGenerator.java diff --git a/java/src/org/broadinstitute/sting/playground/utils/GenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/utils/GenotypeLikelihoods.java rename to java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java diff --git a/java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGGenotypeCall.java similarity index 100% rename from java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java rename to java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGGenotypeCall.java diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyper.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java rename to java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyper.java diff --git a/java/src/org/broadinstitute/sting/utils/genotype/calls/GenotypeCall.java b/java/src/org/broadinstitute/sting/utils/genotype/GenotypeCall.java similarity index 100% rename from java/src/org/broadinstitute/sting/utils/genotype/calls/GenotypeCall.java rename to java/src/org/broadinstitute/sting/utils/genotype/GenotypeCall.java diff --git a/java/src/org/broadinstitute/sting/utils/genotype/GenotypeGenerator.java b/java/src/org/broadinstitute/sting/utils/genotype/GenotypeGenerator.java deleted file mode 100644 index 231a4f1bb..000000000 --- a/java/src/org/broadinstitute/sting/utils/genotype/GenotypeGenerator.java +++ /dev/null @@ -1,26 +0,0 @@ -package org.broadinstitute.sting.utils.genotype; - -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.ReadBackedPileup; - - -/** - * - * @author aaron - * - * Class GenotypeFactory - * - * Create genotypes, given certain pileup information - */ -public interface GenotypeGenerator { - - /** - * given all the data associated with a locus, make a genotypeLocus object containing the likelihoods and posterior probs - * - * @param tracker contains the reference meta data for this location, which may contain relevent information like dpSNP or hapmap information - * @param ref the reference base - * @param pileup a pileup of the reads, containing the reads and their offsets - * @return a GenotypeLocus, containing each of the genotypes and their associated likelihood and posterior prob values - */ - public org.broadinstitute.sting.utils.genotype.calls.GenotypeCall callGenotypes(RefMetaDataTracker tracker, char ref, ReadBackedPileup pileup); -}