Push core / playground lower into the tree.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a

build.xml

@@ -11,31 +11,17 @@
   </condition>
 
   <!-- set global properties for this build -->
-  <property name="build" location="build"/>
-  <property name="dist" location="dist"/>
-  <property name="lib"  location="lib"/>
-  <property name="javadoc" location="javadoc" />
-
   <path id="thirdparty.dependencies">
-    <fileset dir="${lib}" includes="*.jar" />
+    <fileset dir="lib" includes="*.jar" />
   </path>
 
-  <path id="core.classpath">
+  <path id="source">
-    <path refid="thirdparty.dependencies" />
+    <dirset dir="java/src">
-  </path>
+      <patternset>
-
+        <include name="org/broadinstitute/sting/*" />
-  <path id="playground.classpath">
+        <exclude name="**/playground/**" unless="target.is.playground" />
-    <path refid="thirdparty.dependencies" />
+      </patternset>
-    <fileset dir="${build}" includes="**/*.class" />
+    </dirset>
-  </path>
-
-  <path id="core.srcdir">
-    <dirset dir="core/java/src"/>
-  </path>
-
-  <path id="playground.srcdir">
-    <path refid="core.srcdir" />
-    <dirset dir="playground/java/src" />
   </path>
 
   <!-- ivy properties -->
@@ -69,79 +55,77 @@
     <echo message="Compiling module ${target}" />
 
     <!-- Create the build directory structure used by compile -->
-    <mkdir dir="${build}" />
+    <mkdir dir="build" />
   </target>
 
   <target name="compile" depends="init,resolve"
           description="compile the source">
-    <!-- Compile the java code from ${src} into ${build} -->
+    <!-- Compile the java code from ${src} into build -->
-    <javac destdir="${build}" classpathref="${target}.classpath"
+    <javac destdir="build" classpathref="thirdparty.dependencies"
            debug="true" debuglevel="lines,vars,source">
-       <src refid="${target}.srcdir" />
+       <src refid="source" />
     </javac>
   </target>
 
   <target name="dist" depends="compile"
           description="generate the distribution" >
-    <mkdir dir="${dist}"/>
+    <mkdir dir="dist"/>
 
-    <copy todir="${dist}">
+    <copy todir="dist">
-      <fileset dir="${lib}" includes="*.jar" />
+      <fileset dir="lib" includes="*.jar" />
     </copy>
 
-    <jar jarfile="${dist}/StingUtils.jar">
+    <jar jarfile="dist/StingUtils.jar">
-      <fileset dir="${build}" includes="org/broadinstitute/sting/utils/**" />
+      <fileset dir="build" includes="**/utils/**/*.class" />
     </jar>
 
-    <jar jarfile="${dist}/GenomeAnalysisTK.jar">
+    <jar jarfile="dist/GenomeAnalysisTK.jar">
-      <fileset dir="${build}" includes="org/broadinstitute/sting/gatk/**" />
+      <fileset dir="build" includes="**/gatk/**/*.class" />
       <manifest>
         <attribute name="Main-Class" value="org.broadinstitute.sting.gatk.GenomeAnalysisTK" />
       </manifest>
     </jar>
 
-    <!-- Call special distribution methods for the playground.  Will not run if target isn't playground -->  
+    <jar jarfile="dist/FourBaseCaller.jar" whenmanifestonly="skip">
-    <antcall target="dist.playground"/>
+      <fileset dir="build" includes="**/fourbasecaller/**/*.class" />
-
-    <pathconvert property="jar.classpath" pathsep=" ">
-      <flattenmapper />
-      <fileset dir="${dist}" includes="*.jar" />
-    </pathconvert>
-
-    <jar jarfile="${dist}/StingUtils.jar" update="true">
       <manifest>
-        <attribute name="Class-Path" value="${jar.classpath}" />
+        <attribute name="Main-Class" value="org.broadinstitute.sting.playground.fourbasecaller.FourBaseCaller" />
       </manifest>
     </jar>
 
-    <jar jarfile="${dist}/GenomeAnalysisTK.jar" update="true">
+    <jar jarfile="dist/Playground.jar" whenmanifestonly="skip">
-      <manifest>
+      <fileset dir="build">
-        <attribute name="Class-Path" value="${jar.classpath}" />
+        <include name="**/*.class" />
-      </manifest>
+        <exclude name="**/utils/**" />
-    </jar>
+        <exclude name="**/gatk/**" />
-
+        <exclude name="**/fourbasecaller/**" />
-    <jar jarfile="${dist}/FourBaseCaller.jar" basedir="${build}">
-      <manifest>
-        <attribute name="Class-Path" value="${jar.classpath}" />
-        <attribute name="Main-Class" value="org.broadinstitute.sting.projects.fourbasecaller.FourBaseCaller" />
-      </manifest>
-    </jar>
-  </target>
-
-  <target name="dist.playground" if="target.is.playground">
-    <jar jarfile="${dist}/Playground.jar">
-      <fileset dir="${build}">
-        <exclude name="org/broadinstitute/sting/utils/**" />
-        <exclude name="org/broadinstitute/sting/gatk/**" />
       </fileset>
     </jar>
 
     <pathconvert property="jar.classpath" pathsep=" ">
       <flattenmapper />
-      <fileset dir="${dist}" includes="*.jar" />
+      <fileset dir="dist" includes="*.jar" />
     </pathconvert>
 
-    <jar jarfile="${dist}/Playground.jar" update="true">
+    <jar jarfile="dist/StingUtils.jar" update="true">
+      <manifest>
+        <attribute name="Class-Path" value="${jar.classpath}" />
+      </manifest>
+    </jar>
+
+    <jar jarfile="dist/GenomeAnalysisTK.jar" update="true">
+      <manifest>
+        <attribute name="Class-Path" value="${jar.classpath}" />
+      </manifest>
+    </jar>
+
+    <jar jarfile="dist/FourBaseCaller.jar" update="true" whenmanifestonly="skip">
+      <manifest>
+        <attribute name="Class-Path" value="${jar.classpath}" />
+      </manifest>
+    </jar>
+
+    <jar jarfile="dist/Playground.jar" update="true" whenmanifestonly="skip">
       <manifest>
         <attribute name="Class-Path" value="${jar.classpath}" />
       </manifest>
@@ -149,14 +133,15 @@
   </target>
 
   <target name="javadoc">
-    <mkdir dir="${javadoc}" />
+    <mkdir dir="javadoc" />
-    <javadoc sourcepathref="${target}.srcdir" destdir="${javadoc}" />
+    <javadoc sourcepathref="${target}.srcdir" destdir="javadoc" />
   </target>
 
   <target name="clean"
           description="clean up" >
-    <delete dir="${build}"/>
+    <delete dir="out" />
-    <delete dir="${dist}"/>
+    <delete dir="build" />
-    <delete dir="${lib}" />
+    <delete dir="dist" />
+    <delete dir="lib" />
   </target>
 </project>

java/src/org/broadinstitute/sting/playground/ValidateSAM.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting;
+package org.broadinstitute.sting.playground.playground;
 
 import net.sf.samtools.*;
 import net.sf.samtools.SAMFileReader.ValidationStringency;

java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseCaller.java

@@ -1,11 +1,11 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
 import java.io.File;
 import java.util.Vector;
 import java.lang.Math;
 
-import org.broadinstitute.sting.illumina.FirecrestFileParser;
+import org.broadinstitute.sting.playground.illumina.FirecrestFileParser;
-import org.broadinstitute.sting.illumina.FourIntensity;
+import org.broadinstitute.sting.playground.illumina.FourIntensity;
 import cern.colt.matrix.linalg.Algebra;
 import cern.colt.matrix.DoubleMatrix1D;
 import cern.colt.matrix.DoubleFactory1D;

java/src/org/broadinstitute/sting/playground/fourbasecaller/ManyNucleotideSequences.java

@@ -1,9 +1,9 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
 import java.io.File;
 import java.util.Vector;
 
-import org.broadinstitute.sting.projects.fourbasecaller.NucleotideSequence;
+import org.broadinstitute.sting.playground.fourbasecaller.NucleotideSequence;
 
 import edu.mit.broad.picard.reference.ReferenceSequence;
 import edu.mit.broad.picard.reference.ReferenceSequenceFile;

java/src/org/broadinstitute/sting/playground/fourbasecaller/Nucleotide.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
 import java.lang.String;
 

java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideChannelCovariances.java

@@ -1,9 +1,9 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
 import cern.colt.matrix.DoubleFactory2D;
 import cern.colt.matrix.DoubleMatrix2D;
 import cern.colt.matrix.linalg.Algebra;
-import org.broadinstitute.sting.illumina.FourIntensity;
+import org.broadinstitute.sting.playground.illumina.FourIntensity;
 
 public class NucleotideChannelCovariances {
     private DoubleMatrix2D[] covs;

java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideChannelMeans.java

@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
-import org.broadinstitute.sting.illumina.FourIntensity;
+import org.broadinstitute.sting.playground.illumina.FourIntensity;
 
 public class NucleotideChannelMeans {
     private FourIntensity[] sigs;

java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideSequence.java

@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
-import org.broadinstitute.sting.projects.fourbasecaller.Nucleotide;
+import org.broadinstitute.sting.playground.fourbasecaller.Nucleotide;
 
 import java.lang.String;
 import java.util.Vector;

java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk;
+package org.broadinstitute.sting.playground.gatk;
 
 import net.sf.samtools.SAMSequenceRecord;
 import edu.mit.broad.picard.cmdline.CommandLineProgram;

java/src/org/broadinstitute/sting/playground/gatk/iterators/SingleLocusIterator.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.iterators;
+package org.broadinstitute.sting.playground.gatk.iterators;
 
 import net.sf.samtools.util.CloseableIterator;
 import net.sf.samtools.SAMRecord;

java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java

@@ -1,7 +1,7 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
 
 /**

java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java

@@ -1,11 +1,11 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.walkers.AlleleFrequencyWalker;
 import org.broadinstitute.sting.gatk.walkers.BasicLociWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.utils.AlleleFrequencyEstimate;
+import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
+import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
 
 import java.util.List;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java

@@ -1,10 +1,10 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 //import org.broadinstitute.sting.gatk.iterators.LocusIterator;
 import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.utils.AlleleFrequencyEstimate;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.utils.AlleleFrequencyEstimate;
+import org.broadinstitute.sting.gatk.walkers.BasicLociWalker;
+import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;

java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java

@@ -1,7 +1,8 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java

@@ -1,7 +1,7 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
 
 /**

java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java

@@ -1,7 +1,8 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java

@@ -1,7 +1,8 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java

@@ -1,8 +1,9 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.gatk.walkers.BasicLociWalker;
 import org.broadinstitute.sting.utils.Utils;
 import net.sf.samtools.SAMRecord;
 

java/src/org/broadinstitute/sting/playground/illumina/AbstractFirecrestFileParser.java

@@ -8,7 +8,7 @@
 * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
 */
 //package edu.mit.broad.picard.illumina;
-package org.broadinstitute.sting.illumina;
+package org.broadinstitute.sting.playground.illumina;
 
 import edu.mit.broad.picard.util.BasicTextFileParser;
 

java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java

@@ -7,7 +7,7 @@
 * This software is supplied without any warranty or guaranteed support whatsoever. Neither
 * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
 */
-package org.broadinstitute.sting.illumina;
+package org.broadinstitute.sting.playground.illumina;
 
 import edu.mit.broad.picard.util.PasteParser;
 import edu.mit.broad.picard.util.FormatUtil;

java/src/org/broadinstitute/sting/playground/illumina/FirecrestFilenameComparator.java

@@ -8,7 +8,7 @@
 * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
 */
 //package edu.mit.broad.picard.illumina;
-package org.broadinstitute.sting.illumina;
+package org.broadinstitute.sting.playground.illumina;
 
 import java.io.File;
 import java.util.Comparator;

java/src/org/broadinstitute/sting/playground/illumina/FirecrestReadData.java

@@ -7,7 +7,7 @@
 * This software is supplied without any warranty or guaranteed support whatsoever. Neither
 * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
 */
-package org.broadinstitute.sting.illumina;
+package org.broadinstitute.sting.playground.illumina;
 
 /**
  * Holds all the Firecrest-level data we need (so far) about an individual read.

java/src/org/broadinstitute/sting/playground/illumina/FourIntensity.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.illumina;
+package org.broadinstitute.sting.playground.illumina;
 
 import java.util.StringTokenizer;
 

java/src/org/broadinstitute/sting/playground/indels/ConsensusSequence.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import org.broadinstitute.sting.utils.Pair;
 

java/src/org/broadinstitute/sting/playground/indels/DiscardingPileReceiver.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import net.sf.samtools.SAMRecord;
 

java/src/org/broadinstitute/sting/playground/indels/DiscardingReceiver.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import net.sf.samtools.SAMRecord;
 

java/src/org/broadinstitute/sting/playground/indels/Indel.java

@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
-import org.broadinstitute.sting.utils.Interval;
+import org.broadinstitute.sting.playground.utils.Interval;
 
 /**  This class represents an indel as an interval with respect to the <i>original</i> reference and, in addition,
  * stores the indel type ( (I)nsertion or (D)eletion ) and can return meaningful event size (see below).

java/src/org/broadinstitute/sting/playground/indels/IndelInspector.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.io.File;
 import java.util.List;

java/src/org/broadinstitute/sting/playground/indels/IndelRecordPileCollector.java

@@ -1,10 +1,10 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.*;
 
 
-import org.broadinstitute.sting.indels.Indel.IndelType;
+import org.broadinstitute.sting.playground.indels.Indel.IndelType;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.playground.utils.*;
 import net.sf.samtools.*;
 
 /** Ultimately, this class is a splitter for a stream of alignment records. It detects putative indels, or

java/src/org/broadinstitute/sting/playground/indels/IndexedSequence.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.ArrayList;
 import java.util.Hashtable;

java/src/org/broadinstitute/sting/playground/indels/IntervalComparator.java

@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
-import org.broadinstitute.sting.utils.Interval;
+import org.broadinstitute.sting.playground.utils.Interval;
 
 
 public class IntervalComparator implements java.util.Comparator<Interval> {

java/src/org/broadinstitute/sting/playground/indels/KmerCodeIterator.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.Iterator;
 

java/src/org/broadinstitute/sting/playground/indels/MSAColumn.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.List;
 import java.util.ArrayList;

java/src/org/broadinstitute/sting/playground/indels/Matrix.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 public class Matrix<T> {
 	private int nRows;

java/src/org/broadinstitute/sting/playground/indels/MultipleAlignment.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.*;
 import org.broadinstitute.sting.utils.Utils;

java/src/org/broadinstitute/sting/playground/indels/PairwiseAlignment.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.HashSet;
 import java.util.List;

java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import net.sf.samtools.SAMRecord;
 

java/src/org/broadinstitute/sting/playground/indels/RecordPileReceiver.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import net.sf.samtools.SAMRecord;
 

java/src/org/broadinstitute/sting/playground/indels/RecordReceiver.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import net.sf.samtools.SAMRecord;
 

java/src/org/broadinstitute/sting/playground/indels/SequencePile.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.List;
 import java.util.ArrayList;

java/src/org/broadinstitute/sting/playground/indels/StrictlyUpperTriangularMatrix.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 public class StrictlyUpperTriangularMatrix extends SymmetricMatrix {
 

java/src/org/broadinstitute/sting/playground/indels/SymmetricMatrix.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 /**
  * Created by IntelliJ IDEA.

java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java

@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
-import org.broadinstitute.sting.gatk.walkers.AlleleFrequencyWalker;
+import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
 
 public class AlleleFrequencyEstimate {
     //AlleleFrequencyEstimate();

java/src/org/broadinstitute/sting/playground/utils/CountedObject.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
 /** Utility class that makes working with counted objects slightly easier (and faster). 
  * Consider a "generic" counter representation as Map<Object,Integer>: updating the counter would require

java/src/org/broadinstitute/sting/playground/utils/CountedObjectComparatorAdapter.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
 
 /** Support class for counted objects. This comparator is an adapter: it is initialized with an arbitrary

java/src/org/broadinstitute/sting/playground/utils/Interval.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
 /**
  * Created by IntelliJ IDEA.
@@ -48,12 +48,12 @@ public interface Interval {
       * @param i Another interval
      * @return true iff intervals overlap
      */
-    public boolean overlapsP(org.broadinstitute.sting.utils.Interval i);
+    public boolean overlapsP(org.broadinstitute.sting.playground.utils.Interval i);
 
     /** Returns true if this interval does not overlap with i as judjed by getStart() and getStop() positions of the
      * two interval objects.
       * @param i Another interval
      * @return true iff intervals do not overlap
      */
-    public boolean disjointP(org.broadinstitute.sting.utils.Interval i);
+    public boolean disjointP(org.broadinstitute.sting.playground.utils.Interval i);
 }

java/src/org/broadinstitute/sting/playground/utils/SimpleInterval.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
 /**
  * Created by IntelliJ IDEA.
@@ -59,7 +59,7 @@ public class SimpleInterval implements Interval {
      * @return true iff intervals overlap
      */
     @Override
-    public boolean overlapsP(org.broadinstitute.sting.utils.Interval i) {
+    public boolean overlapsP(org.broadinstitute.sting.playground.utils.Interval i) {
         return ! disjointP(i);
     }
 
@@ -69,7 +69,7 @@ public class SimpleInterval implements Interval {
      * @return true iff intervals do not overlap
      */
     @Override
-    public boolean disjointP(org.broadinstitute.sting.utils.Interval i) {
+    public boolean disjointP(org.broadinstitute.sting.playground.utils.Interval i) {
         return ( i.getStop() < this.m_start || i.getStart() > this.m_stop );
     }
 }

java/src/org/broadinstitute/sting/playground/utils/WhitespaceTextFileParser.java

@@ -7,7 +7,7 @@
 * This software is supplied without any warranty or guaranteed support whatsoever. Neither
 * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
 */
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
 import edu.mit.broad.picard.util.BasicTextFileParser;