diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java index b40237386..4385e719f 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer; +package org.broadinstitute.sting.gatk.walkers.analyzeannotations; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java rename to java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java index bcedfc156..178f73c1a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer; +package org.broadinstitute.sting.gatk.walkers.analyzeannotations; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.utils.BaseUtils; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDatum.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDatum.java rename to java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java index fb321b899..063cf3e62 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDatum.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer; +package org.broadinstitute.sting.gatk.walkers.analyzeannotations; import org.broadinstitute.sting.utils.StingException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 9d2e493a0..a28152f06 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -47,11 +47,8 @@ import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.playground.gatk.walkers.annotator.GenomicAnnotation; -import org.broadinstitute.sting.playground.gatk.walkers.annotator.JoinTable; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; +import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.*; import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.classloader.PackageUtils; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcid.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/AminoAcid.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcid.java rename to java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/AminoAcid.java index 54c2ac1ef..0d0b906e0 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcid.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/AminoAcid.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.annotator; +package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; /** * Represents a single amino acid. diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcidTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/AminoAcidTable.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcidTable.java rename to java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/AminoAcidTable.java index 41541b01c..c10eb5dd7 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcidTable.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/AminoAcidTable.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.annotator; +package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; import java.util.HashMap; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java rename to java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java index 93ce8a119..464111cdb 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.annotator; +package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; import java.util.*; import java.util.Map.Entry; @@ -159,7 +159,7 @@ public class GenomicAnnotation implements InfoFieldAnnotation { boolean matchFound = false; for(String hapAlt : hapAltValue.split("[,\\\\/:|]")) { if(!positiveStrand) { - hapAlt = BaseUtils.simpleReverseComplement(hapAlt); + hapAlt = new String(BaseUtils.simpleReverseComplement(hapAlt.getBytes())); } if(!hapAlt.isEmpty() && vcAlt.basesMatch(hapAlt)) { @@ -228,9 +228,9 @@ public class GenomicAnnotation implements InfoFieldAnnotation { /** * Combines the 2 values into a full key. - * @param rodBindingName - * @param columnName - * @return + * @param rodBindingName -B name + * @param columnName column name + * @return info field key */ public static String generateInfoFieldKey(String rodBindingName, String columnName ) { return rodBindingName + '.' + columnName; @@ -241,7 +241,7 @@ public class GenomicAnnotation implements InfoFieldAnnotation { /** * Replaces any characters that are not allowed in the info field of a VCF file. * - * @param value + * @param value info field value * @return the value with any illegal characters replaced by legal ones. */ private static String scrubInfoFieldValue(String value) { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java rename to java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java index 0d6d8e139..8ac285753 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java @@ -24,7 +24,7 @@ */ -package org.broadinstitute.sting.playground.gatk.walkers.annotator; +package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; import java.io.IOException; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/JoinTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/JoinTable.java rename to java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java index d9e55c03e..854139d86 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/JoinTable.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.annotator; +package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; import java.io.BufferedReader; import java.io.FileReader; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/JoinTableParser.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/JoinTableParser.java rename to java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java index d4128f5b9..b624b2dfb 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/JoinTableParser.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.annotator; +package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; import java.io.BufferedReader; import java.io.IOException; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToInfo.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java rename to java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToInfo.java index a32766e3a..b7c9f92d7 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToInfo.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.annotator; +package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; import java.io.*; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java index dcc413a19..9261304fa 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.beagle; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Genotype; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java index 89961ec08..4f83c8dd7 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.beagle; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Genotype; diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java similarity index 75% rename from java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java rename to java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java index 32bf7bb2f..35b5a2e37 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java @@ -1,4 +1,29 @@ -package org.broadinstitute.sting.playground.gatk.walkers; +/* + * Copyright (c) 2010. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.gatk.walkers; import org.broadinstitute.sting.WalkerTest; import org.junit.Test; diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java similarity index 96% rename from java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java rename to java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java index 4891a3e1d..c0bc2150f 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.annotator; +package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator; import java.util.Arrays; diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java similarity index 97% rename from java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java rename to java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java index 4128a3f13..cc81f262f 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.beagle; import org.broadinstitute.sting.WalkerTest; import org.junit.Test;