From 97f60dbc4b3d35bbdf180c50a685838a44ea2cf4 Mon Sep 17 00:00:00 2001 From: chartl Date: Fri, 29 Jan 2010 22:50:03 +0000 Subject: [PATCH] Moving stuff around. ( core;playground ) ----> ( oneoffs ). I've been a bad boy, sullying the core codebase. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2745 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/refdata/ReferenceOrderedData.java | 3 ++- .../{gatk => oneoffprojects}/refdata/HapmapVCFROD.java | 10 +++++----- .../varianteval/multisample/LocusConcordanceInfo.java | 2 +- .../multisample/MultiSampleConcordanceSet.java | 2 +- .../multisample/MultiSampleConcordanceWalker.java | 2 +- .../multisample/VCFConcordanceCalculator.java | 2 +- 6 files changed, 11 insertions(+), 10 deletions(-) rename java/src/org/broadinstitute/sting/{gatk => oneoffprojects}/refdata/HapmapVCFROD.java (94%) rename java/src/org/broadinstitute/sting/{playground/gatk => oneoffprojects}/walkers/varianteval/multisample/LocusConcordanceInfo.java (96%) rename java/src/org/broadinstitute/sting/{playground/gatk => oneoffprojects}/walkers/varianteval/multisample/MultiSampleConcordanceSet.java (96%) rename java/src/org/broadinstitute/sting/{playground/gatk => oneoffprojects}/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java (98%) rename java/src/org/broadinstitute/sting/{playground/gatk => oneoffprojects}/walkers/varianteval/multisample/VCFConcordanceCalculator.java (97%) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java index 9c8f143b4..8c06969ce 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java @@ -1,6 +1,7 @@ package org.broadinstitute.sting.gatk.refdata; import org.apache.log4j.Logger; +import org.broadinstitute.sting.oneoffprojects.refdata.HapmapVCFROD; import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.Utils; @@ -77,7 +78,7 @@ public class ReferenceOrderedData implements addModule("GLF", RodGLF.class); addModule("VCF", RodVCF.class); addModule("PicardDbSNP", rodPicardDbSNP.class); - addModule("HapmapVCF",HapmapVCFROD.class); + addModule("HapmapVCF", HapmapVCFROD.class); } diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/HapmapVCFROD.java b/java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java similarity index 94% rename from java/src/org/broadinstitute/sting/gatk/refdata/HapmapVCFROD.java rename to java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java index 7a6f9d490..6169f7462 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/HapmapVCFROD.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java @@ -1,5 +1,8 @@ -package org.broadinstitute.sting.gatk.refdata; +package org.broadinstitute.sting.oneoffprojects.refdata; +import org.broadinstitute.sting.gatk.refdata.BasicReferenceOrderedDatum; +import org.broadinstitute.sting.gatk.refdata.RodVCF; +import org.broadinstitute.sting.gatk.refdata.VariationRod; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.genotype.DiploidGenotype; @@ -12,16 +15,13 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord; import java.io.File; import java.io.FileNotFoundException; -import java.io.IOException; import java.util.Iterator; import java.util.List; -/** +/* * Created by IntelliJ IDEA. * User: chartl * Date: Jan 29, 2010 - * Time: 8:57:54 AM - * To change this template use File | Settings | File Templates. */ public class HapmapVCFROD extends BasicReferenceOrderedDatum implements VariationRod, VariantBackedByGenotype, Iterator { // This is a (hopefully temporary) wrapper class for certain VCF files that we want to protect from diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/LocusConcordanceInfo.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/LocusConcordanceInfo.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/LocusConcordanceInfo.java rename to java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/LocusConcordanceInfo.java index 06b6f11f2..b469cd59b 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/LocusConcordanceInfo.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/LocusConcordanceInfo.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample; +package org.broadinstitute.sting.oneoffprojects.walkers.varianteval.multisample; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceSet.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceSet.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceSet.java rename to java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceSet.java index 441f503ed..7bfd72155 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceSet.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceSet.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample; +package org.broadinstitute.sting.oneoffprojects.walkers.varianteval.multisample; import java.util.HashSet; import java.util.Set; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java rename to java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java index 04b62e566..4e6588805 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample; +package org.broadinstitute.sting.oneoffprojects.walkers.varianteval.multisample; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/VCFConcordanceCalculator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/VCFConcordanceCalculator.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/VCFConcordanceCalculator.java rename to java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/VCFConcordanceCalculator.java index d5cad1c04..5f9d401bb 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/multisample/VCFConcordanceCalculator.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/VCFConcordanceCalculator.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample; +package org.broadinstitute.sting.oneoffprojects.walkers.varianteval.multisample; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;