Moving supported tools to core

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4127 348d0f76-0448-11de-a6fe-93d51630548a

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;

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;

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;
 

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.*;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.*;
-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.utils.StingException;
 import org.broadinstitute.sting.utils.classloader.PackageUtils;
 

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.

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;
 

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 rodBindingName -B name
-     * @param columnName
+     * @param columnName     column name
-     * @return
+     * @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) {

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.*;

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;

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;

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;

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;

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;

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;

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;

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;