Renaming of ATK to GATK, the genome analysis TK.

Also added several more layers of error checking 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@54 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -1,7 +1,8 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.atk.modules;
 
-import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.atk.LocusIterator;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.atk.LocusContext;
+import org.broadinstitute.sting.utils.ReferenceOrderedDatum;
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;

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

@@ -1,8 +1,8 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.atk.modules;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.atk.ReadWalker;
-import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.atk.LocusContext;
 
 /**
  * Created by IntelliJ IDEA.
@@ -27,7 +27,7 @@ public class BaseQualityHistoWalker implements ReadWalker<Integer, Integer> {
         return true;    // We are keeping all the reads
     }
 
-    // Map over the org.broadinstitute.sting.gatk.LocusContext
+    // Map over the org.broadinstitute.sting.atk.LocusContext
     public Integer map(LocusContext context, SAMRecord read) {
         for ( byte qual : read.getBaseQualities() ) {
             //System.out.println(qual);

playground/java/src/org/broadinstitute/sting/gatk/modules/BasicLociWalker.java

@@ -1,8 +1,10 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.atk.modules;
 
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.atk.LocusWalker;
-import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.atk.LocusIterator;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.atk.LocusContext;
+import org.broadinstitute.sting.utils.ReferenceOrderedDatum;
+import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 
@@ -25,8 +27,7 @@ public abstract class BasicLociWalker<MapType, ReduceType> implements LocusWalke
         return true;    // We are keeping all the reads
     }
 
-    public void onTraversalDone() {
+    public void onTraveralDone() {
-        ;
     }
 
     // These three capabilities must be overidden

playground/java/src/org/broadinstitute/sting/gatk/modules/BasicReadWalker.java

@@ -1,8 +1,8 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.atk.modules;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.atk.LocusContext;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.atk.ReadWalker;
 
 /**
  * Created by IntelliJ IDEA.
@@ -20,8 +20,8 @@ public abstract class BasicReadWalker<MapType, ReduceType> implements ReadWalker
         return true;
     }
 
-    public void onTraversalDone() {
+    public void onTraveralDone() {
-        ;
+
     }
 
     // Three basic abstract function that *must* be overridden

playground/java/src/org/broadinstitute/sting/gatk/modules/CountLociWalker.java

@@ -1,7 +1,7 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.atk.modules;
 
-import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.atk.LocusContext;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.utils.ReferenceOrderedDatum;
 
 import java.util.List;
 

playground/java/src/org/broadinstitute/sting/gatk/modules/CountReadsWalker.java

@@ -1,7 +1,7 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.atk.modules;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.atk.LocusContext;
 
 public class CountReadsWalker extends BasicReadWalker<Integer, Integer> {
     public Integer map(LocusContext context, SAMRecord read) {

playground/java/src/org/broadinstitute/sting/gatk/modules/DepthOfCoverageWalker.java

@@ -1,10 +1,12 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.atk.modules;
 
-import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.atk.LocusContext;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.utils.ReferenceOrderedDatum;
 
 import java.util.List;
 
+import net.sf.samtools.SAMRecord;
+
 /**
  * Created by IntelliJ IDEA.
  * User: mdepristo

playground/java/src/org/broadinstitute/sting/gatk/modules/NullWalker.java

@@ -1,8 +1,12 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.atk.modules;
 
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.atk.LocusWalker;
-import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.atk.LocusIterator;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.atk.LocusContext;
+import org.broadinstitute.sting.utils.ReferenceOrderedDatum;
+import org.broadinstitute.sting.utils.rodDbSNP;
+import org.broadinstitute.sting.utils.Utils;
+import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 
@@ -20,7 +24,7 @@ public class NullWalker implements LocusWalker<Integer, Integer> {
         return true;    // We are keeping all the reads
     }
 
-    // Map over the org.broadinstitute.sting.gatk.LocusContext
+    // Map over the org.broadinstitute.sting.atk.LocusContext
     public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) 
     {
         return 1;
@@ -36,6 +40,6 @@ public class NullWalker implements LocusWalker<Integer, Integer> {
         return 0;
     }
 
-    public void onTraversalDone() {
+    public void onTraveralDone() {
     }
 }

playground/java/src/org/broadinstitute/sting/gatk/modules/PileupWalker.java

@@ -1,8 +1,11 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.atk.modules;
 
-import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.atk.LocusWalker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.atk.LocusIterator;
-import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.atk.LocusContext;
+import org.broadinstitute.sting.utils.ReferenceOrderedDatum;
+import org.broadinstitute.sting.utils.rodDbSNP;
+import org.broadinstitute.sting.utils.Utils;
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;
@@ -14,7 +17,7 @@ import java.util.List;
  * Time: 3:22:14 PM
  * To change this template use File | Settings | File Templates.
  */
-public class PileupWalker extends BasicLociWalker<Integer, Integer> {
+public class PileupWalker implements LocusWalker<Integer, Integer> {
     public void initialize() {
     }
 
@@ -25,7 +28,7 @@ public class PileupWalker extends BasicLociWalker<Integer, Integer> {
         return true;    // We are keeping all the reads
     }
 
-    // Map over the org.broadinstitute.sting.gatk.LocusContext
+    // Map over the org.broadinstitute.sting.atk.LocusContext
     public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
         //System.out.printf("Reads %s:%d %d%n", context.getContig(), context.getPosition(), context.getReads().size());
         //for ( SAMRecord read : context.getReads() ) {
@@ -81,4 +84,7 @@ public class PileupWalker extends BasicLociWalker<Integer, Integer> {
     public Integer reduce(Integer value, Integer sum) {
         return value + sum;
     }
+
+    public void onTraveralDone() {
+    }
 }

playground/java/src/org/broadinstitute/sting/gatk/modules/PrintReadsWalker.java

@@ -1,7 +1,7 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.atk.modules;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.atk.LocusContext;
 
 public class PrintReadsWalker extends BasicReadWalker<Integer, Integer> {
     public Integer map(LocusContext context, SAMRecord read) {

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

@@ -1,8 +1,10 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.atk.modules;
 
-import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.atk.LocusWalker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.atk.LocusIterator;
-import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.atk.LocusContext;
+import org.broadinstitute.sting.utils.ReferenceOrderedDatum;
+import org.broadinstitute.sting.utils.rodDbSNP;
 import org.broadinstitute.sting.utils.Utils;
 import net.sf.samtools.SAMRecord;
 
@@ -11,7 +13,13 @@ import java.util.List;
 // Draft single sample genotyper
 // j.maguire 3-7-2009
 
-public class SingleSampleGenotyper extends BasicLociWalker<Integer, Integer> {
+public class SingleSampleGenotyper implements LocusWalker<Integer, Integer> {
+    public void initialize() {
+    }
+
+    public String walkerType() { return "ByLocus"; }
+
+    // Do we actually want to operate on the context?
     public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
         return true;    // We are keeping all the reads
     }
@@ -78,7 +86,7 @@ public class SingleSampleGenotyper extends BasicLociWalker<Integer, Integer> {
 
     }
 
-    // Map over the org.broadinstitute.sting.gatk.LocusContext
+    // Map over the org.broadinstitute.sting.atk.LocusContext
     public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
         //System.out.printf("Reads %s:%d %d%n", context.getContig(), context.getPosition(), context.getReads().size());
         //for ( SAMRecord read : context.getReads() ) {
@@ -97,7 +105,7 @@ public class SingleSampleGenotyper extends BasicLociWalker<Integer, Integer> {
         {
             if ( datum != null ) 
             {
-                if ( datum instanceof rodDbSNP)
+                if ( datum instanceof rodDbSNP) 
                 {
                     rodDbSNP dbsnp = (rodDbSNP)datum;
                     rodString += dbsnp.toMediumString();
@@ -136,4 +144,7 @@ public class SingleSampleGenotyper extends BasicLociWalker<Integer, Integer> {
     public Integer reduce(Integer value, Integer sum) {
         return value + sum;
     }
+
+    public void onTraveralDone() {
+    }
 }

playground/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java

@@ -1,213 +0,0 @@
-package org.broadinstitute.sting.gatk.refdata;
-
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.Iterator;
-import java.util.ArrayList;
-import java.util.Collections;
-
-import edu.mit.broad.picard.util.TabbedTextFileParser;
-import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-/**
- * Class for representing arbitrary reference ordered data sets
- *
- * User: mdepristo
- * Date: Feb 27, 2009
- * Time: 10:47:14 AM
- * To change this template use File | Settings | File Templates.
- */
-public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements Iterable<ROD> {
-    private File file = null;
-    private Class<ROD> type = null; // runtime type information for object construction
-
-    public ReferenceOrderedData(File file, Class<ROD> type ) {
-        this.file = file;
-        this.type = type;
-    }
-
-    public RODIterator iterator() {
-        return new RODIterator(new SimpleRODIterator());
-    }
-
-    // ----------------------------------------------------------------------
-    //
-    // Testing
-    //
-    // ----------------------------------------------------------------------
-    public void testMe() {
-        ReferenceOrderedDatum last = null;
-        for ( ReferenceOrderedDatum rec : this ) {
-            if ( last == null || ! last.getLocation().onSameContig(rec.getLocation()) ) {
-                System.out.println(rec.toString());
-            }
-            last = rec;
-        }
-        System.exit(1);
-    }
-
-    // ----------------------------------------------------------------------
-    //
-    // Manipulations of all of the data
-    //
-    // ----------------------------------------------------------------------
-    public ArrayList<ReferenceOrderedDatum> readAll() {
-        ArrayList<ReferenceOrderedDatum> elts = new ArrayList<ReferenceOrderedDatum>();
-        for ( ReferenceOrderedDatum rec : this ) {
-            elts.add(rec);
-        }
-        elts.trimToSize();
-        return elts;
-    }
-
-    public static void sortRODDataInMemory(ArrayList<ReferenceOrderedDatum> data) {
-        Collections.sort(data);
-    }
-
-    public static void write(ArrayList<ReferenceOrderedDatum> data, File output) throws IOException {
-        final FileWriter out = new FileWriter(output);
-
-        for ( ReferenceOrderedDatum rec : data ) {
-            out.write(rec.repl() + "\n");
-        }
-
-        out.close();
-    }
-
-    public boolean validateFile() throws Exception {
-        ReferenceOrderedDatum last = null;
-        for ( ReferenceOrderedDatum rec : this ) {
-             if ( last != null && last.compareTo(rec) == 1 ) {
-                 // It's out of order
-                 throw new Exception("Out of order elements at \n" + last.toString() + "\n" + rec.toString());
-             }
-             last = rec;
-        }
-        return true;
-    }
-
-    public void indexFile() {
-        // Fixme -- get access to the linear index system from Jim
-    }
-
-    // ----------------------------------------------------------------------
-    //
-    // Iteration
-    //
-    // ----------------------------------------------------------------------
-    private class SimpleRODIterator implements Iterator<ROD> {
-        //private WhitespaceTextFileParser parser = null;
-        private TabbedTextFileParser parser = null;
-
-        public SimpleRODIterator() {
-            parser = new TabbedTextFileParser(true, file);
-        }
-
-        public boolean hasNext() {
-            return parser.hasNext();
-        }
-
-        public ROD next() {
-            String parts[] = parser.next();
-            return parseLine(parts);
-        }
- 
-        public void remove() {
-            throw new UnsupportedOperationException();
-        }
-    }
-
-    public class RODIterator implements Iterator<ROD> {
-        private PushbackIterator<ROD> it;
-        private ROD prev = null;
-        
-        public RODIterator(SimpleRODIterator it) {
-            this.it = new PushbackIterator<ROD>(it);
-        }
-
-        public boolean hasNext() { return it.hasNext(); }
-        public ROD next() {
-            prev = it.next();
-            return prev; 
-        }
-
-        //
-        // Seeks forward in the file until we reach (or cross) a record at contig / pos
-        // If we don't find anything and cross beyond contig / pos, we return null
-        // Otherwise we return the first object who's start is at pos
-        //
-        public ROD seekForward(final GenomeLoc loc) {
-            return seekForward(loc.getContig(), loc.getStart());
-        }
-
-        protected ROD seekForward(final String contigName, final long pos) {
-            final boolean DEBUG = false; 
-        
-            ROD result = null;
-            
-            if ( DEBUG ) System.out.printf("  *** starting seek to %s %d %s%n", contigName, pos, prev);
-            while ( hasNext() ) {
-                ROD current = next();
-                //System.out.printf("    -> Seeking to %s %d AT %s %d%n", contigName, pos, current.getContig(), current.getStart());
-                int strCmp = GenomeLoc.compareContigs( contigName, prev.getContig() );// contigName.compareTo( prev.getContig() );
-                if ( strCmp == 0 ) {
-                    // The contigs are equal
-                    if ( current.getStart() > pos ) {
-                        // There was nothing to find, push back next and return null
-                        it.pushback(current);
-                        break;
-                    }
-                    else if ( pos == current.getStart() ) {
-                        // We found a record at contig / pos, return it
-                        result = current;
-                        break;
-                    }
-                }
-                else if ( strCmp < 0 ) {
-                    if ( DEBUG ) System.out.printf("    -> Jumped to contig %s%n", contigName);
-                    // We've gone past the desired contig, break
-                    it.pushback(current);
-                    break;
-                }
-            }
-
-            if ( DEBUG ) {
-                if ( result == null )
-                    ;
-                    //System.out.printf("    --- seek result to %s %d is NULL%n", contigName, pos);
-                else
-                    System.out.printf("    ### Found %s %d%n", result.getContig(), result.getStart());
-            }
-            
-
-             // we ran out of elements or found something
-            return result;
-        }
-
-        public void remove() {
-            throw new UnsupportedOperationException();
-        }
-    }
-
-    // ----------------------------------------------------------------------
-    //
-    // Parsing
-    //
-    // ----------------------------------------------------------------------
-    ROD parseLine(final String[] parts) {
-        //System.out.printf("Parsing GFFLine %s%n", Utils.join(" ", parts));
-        try {
-            ROD obj = type.newInstance();
-            obj.parseLine(parts);
-            return obj;
-        } catch ( java.lang.InstantiationException e ) {
-            System.out.println(e);
-            return null; // wow, unsafe!
-        } catch ( java.lang.IllegalAccessException e ) {
-            System.out.println(e);
-            return null; // wow, unsafe!
-        }       
-    }
-}

playground/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java

@@ -1,30 +0,0 @@
-package org.broadinstitute.sting.gatk.refdata;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-/**
- * Created by IntelliJ IDEA.
- * User: mdepristo
- * Date: Feb 27, 2009
- * Time: 10:49:47 AM
- * To change this template use File | Settings | File Templates.
- */
-public abstract class ReferenceOrderedDatum implements Comparable<ReferenceOrderedDatum> {
-
-    public ReferenceOrderedDatum() { }
-
-    public abstract void parseLine(final String[] parts);
-
-    public abstract String toString();
-    public abstract String toSimpleString();
-    public abstract String repl();
-
-    public abstract GenomeLoc getLocation();
-    public int compareTo( ReferenceOrderedDatum that ) {
-        return getLocation().compareTo(that.getLocation());
-    }
-
-    public final String getContig() { return getLocation().getContig(); }
-    public final long getStart() { return getLocation().getStart(); }
-    public final long getStop() { return getLocation().getStop(); }
-}

playground/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java

@@ -1,157 +0,0 @@
-package org.broadinstitute.sting.gatk.refdata;
-
-import edu.mit.broad.picard.util.SequenceUtil;
-
-import java.util.*;
-
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-
-/**
- * Example format:
- *   585 chr1 433 433 rs56289060  0  +  - - -/C  genomic  insertion unknown 0  0  unknown  between  1
- *   585 chr1 491 492 rs55998931  0  +  C C C/T  genomic  single   unknown 0 0 unknown exact 1
- *
- * User: mdepristo
- * Date: Feb 27, 2009
- * Time: 10:47:14 AM
- * To change this template use File | Settings | File Templates.
- */
-public class rodDbSNP extends ReferenceOrderedDatum {
-    public GenomeLoc loc;       // genome location of SNP
-                                // Reference sequence chromosome or scaffold
-                                // Start and stop positions in chrom
-
-    public String name;        // Reference SNP identifier or Affy SNP name
-    public String strand;      // Which DNA strand contains the observed alleles
-
-    public String refBases;        // the reference base according to NCBI, in the dbSNP file
-    public String observed;    // The sequences of the observed alleles from rs-fasta files
-
-    public String molType;     // Sample type from exemplar ss
-    public String varType;     // The class of variant (simple, insertion, deletion, range, etc.)
-                                // Can be 'unknown','single','in-del','het','microsatellite','named','mixed','mnp','insertion','deletion'
-    public String validationStatus;    // The validation status of the SNP
-                                        // one of set('unknown','by-cluster','by-frequency','by-submitter','by-2hit-2allele','by-hapmap')
-
-    public double avHet;        // The average heterozygosity from all observations
-    public double avHetSE;      // The Standard Error for the average heterozygosity
-
-    public String func;         // The functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.)
-                                // set('unknown','coding-synon','intron','cds-reference','near-gene-3','near-gene-5',
-                                // 'nonsense','missense','frameshift','untranslated-3','untranslated-5','splice-3','splice-5')
-    public String locType;      // How the variant affects the reference sequence
-                                // enum('range','exact','between','rangeInsertion','rangeSubstitution','rangeDeletion')
-
-    public int weight;          // The quality of the alignment
-
-    // ----------------------------------------------------------------------
-    //
-    // Constructors
-    //
-    // ----------------------------------------------------------------------
-    public rodDbSNP() {}
-
-    // ----------------------------------------------------------------------
-    //
-    // manipulating the SNP information
-    //
-    // ----------------------------------------------------------------------
-    public GenomeLoc getLocation() { return loc; }
-
-    public boolean onFwdStrand() {
-        return strand.equals("+");
-    }
-
-    // Get the reference bases on the forward strand
-    public String getRefBasesFWD() {
-        if ( onFwdStrand() )
-            return refBases;
-        else
-            return SequenceUtil.reverseComplement(refBases);
-    }
-
-    public List<String> getAllelesFWD() {
-        List<String> alleles = null;
-        if ( onFwdStrand() )
-            alleles = Arrays.asList(observed.split("/"));
-        else
-            alleles = Arrays.asList(SequenceUtil.reverseComplement(observed).split("/"));
-
-        //System.out.printf("getAlleles %s on %s %b => %s %n", observed, strand, onFwdStrand(), Utils.join("/", alleles));
-        return alleles;
-    }
-
-    public String getAllelesFWDString() {
-        return Utils.join("/", getAllelesFWD());
-    }
-
-    // ----------------------------------------------------------------------
-    //
-    // What kind of variant are we?
-    //
-    // ----------------------------------------------------------------------
-    public boolean isSNP() { return varType.contains("single"); }
-    public boolean isInsertion() { return varType.contains("insertion"); }
-    public boolean isDeletion() { return varType.contains("deletion"); }
-    public boolean isIndel() { return varType.contains("in-del"); }
-
-    public boolean isHapmap() { return validationStatus.contains("by-hapmap"); }
-    public boolean is2Hit2Allele() { return validationStatus.contains("by-2hit-2allele"); }
-
-    // ----------------------------------------------------------------------
-    //
-    // formatting
-    //
-    // ----------------------------------------------------------------------
-    public String toString() {
-        return String.format("%s\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%f\t%f\t%s\t%s\t%d",
-                getContig(), getStart(), getStop(), name, strand, refBases, observed, molType,
-                varType, validationStatus, avHet, avHetSE, func, locType, weight );
-    }
-
-    public String toSimpleString() {
-        return String.format("%s:%s:%s", name, observed, strand);
-    }
-
-    public String toMediumString() {
-        String s = String.format("%s:%s:%s", getLocation().toString(), name, getAllelesFWDString());
-        if ( isSNP() ) s += ":SNP";
-        if ( isIndel() ) s += ":Indel";
-        if ( isHapmap() ) s += ":Hapmap";
-        if ( is2Hit2Allele() ) s += ":2Hit";
-        return s;        
-    }
-
-    public String repl() {
-        return String.format("%d\t%s\t%d\t%d\t%s\t0\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%f\t%f\t%s\t%s\t%d",
-                585, getContig(), getStart()-1, getStop()-1, name, strand, refBases, refBases, observed, molType,
-                varType, validationStatus, avHet, avHetSE, func, locType, weight );
-    }
-
-    public void parseLine(final String[] parts) {
-        try {
-            String contig = parts[1];
-            long start = Long.parseLong(parts[2]) + 1; // The final is 0 based
-            long stop = Long.parseLong(parts[3]) + 1;  // The final is 0 based
-            loc = new GenomeLoc(contig, start, stop);
-
-            name = parts[4];
-            refBases = parts[5];
-            strand = parts[6];
-            observed = parts[9];
-            molType = parts[10];
-            varType = parts[11];
-            validationStatus = parts[12];
-            avHet = Double.parseDouble(parts[13]);
-            avHetSE = Double.parseDouble(parts[14]);
-            func = parts[15];
-            locType = parts[16];
-            weight = Integer.parseInt(parts[17]);
-        } catch ( RuntimeException e ) {
-            System.out.printf("  Exception caught during parsing GFFLine %s%n", Utils.join(" <=> ", parts));
-            throw e;
-        }
-    }
-}

playground/java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java

@@ -1,113 +0,0 @@
-package org.broadinstitute.sting.gatk.refdata;
-
-import java.util.HashMap;
-
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-/**
- * Class for representing arbitrary reference ordered data sets
- *
- * User: mdepristo
- * Date: Feb 27, 2009
- * Time: 10:47:14 AM
- * To change this template use File | Settings | File Templates.
- */
-public class rodGFF extends ReferenceOrderedDatum {
-    private String contig, source, feature, strand, frame;
-    private long start, stop;
-    private double score;
-    private HashMap<String, String> attributes;
-    
-    // ----------------------------------------------------------------------
-    //
-    // Constructors
-    //
-    // ----------------------------------------------------------------------
-    public rodGFF() {
-        
-    }
-
-    public void setValues(final String contig, final String source, final String feature,
-                          final long start, final long stop, final double score,
-                          final String strand, final String frame, HashMap<String, String> attributes) {
-        this.contig = contig;
-        this.source = source;
-        this.feature = feature;
-        this.start = start;
-        this.stop= stop;
-        this.score = score;
-        this.strand = strand;
-        this.frame = frame;
-        this.attributes = attributes;
-    }
-
-    // ----------------------------------------------------------------------
-    //
-    // Accessors
-    //
-    // ----------------------------------------------------------------------
-    public String getSource() {
-        return source;
-    }
-
-    public String getFeature() {
-        return feature;
-    }
-
-    public String getStrand() {
-        return strand;
-    }
-
-    public String getFrame() {
-        return frame;
-    }
-
-    public double getScore() {
-        return score;
-    }
-
-    public GenomeLoc getLocation() {
-        return new GenomeLoc(contig, start, stop);
-    }
-
-    public String getAttribute(final String key) {
-        return attributes.get(key);
-    }
-
-    // ----------------------------------------------------------------------
-    //
-    // formatting
-    //
-    // ----------------------------------------------------------------------
-    public String toString() {
-        return String.format("%s\t%s\t%s\t%d\t%d\t%f\t%s\t%s", contig, source, feature, start, stop, score, strand, frame);
-    }
-
-    public String repl() {
-        return this.toString();
-    }
-
-    public String toSimpleString() {
-        return String.format("%s", feature);
-    }
-
-    public void parseLine(final String[] parts) {
-        //System.out.printf("Parsing GFFLine %s%n", Utils.join(" ", parts));
-
-        final String contig = parts[0];
-        final String source = parts[1];
-        final String feature = parts[2];
-        final long start = Long.parseLong(parts[3]);
-        final long stop = Long.parseLong(parts[4]);
-
-        double score = Double.NaN;
-        if ( ! parts[5].equals(".") )
-            score = Double.parseDouble(parts[5]);
-
-        final String strand = parts[6];
-        final String frame = parts[7];
-        HashMap<String, String> attributes = null;
-        setValues(contig, source, feature, start, stop, score, strand, frame, attributes);
-    }
-}

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

@@ -1,30 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers;
-
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.LocusContext;
-
-import java.util.List;
-
-/**
- * Created by IntelliJ IDEA.
- * User: mdepristo
- * Date: Feb 22, 2009
- * Time: 2:52:28 PM
- * To change this template use File | Settings | File Templates.
- */
-public interface LocusWalker<MapType, ReduceType> {
-    void initialize();
-    public String walkerType();
-
-    // Do we actually want to operate on the context?
-    boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context);
-
-    // Map over the org.broadinstitute.sting.gatk.LocusContext
-    MapType map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context);
-
-    // Given result of map function
-    ReduceType reduceInit();
-    ReduceType reduce(MapType value, ReduceType sum);
-
-    void onTraversalDone();
-}

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

@@ -1,28 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers;
-
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.LocusContext;
-
-/**
- * Created by IntelliJ IDEA.
- * User: mdepristo
- * Date: Feb 22, 2009
- * Time: 2:52:28 PM
- * To change this template use File | Settings | File Templates.
- */
-public interface ReadWalker<MapType, ReduceType> {
-    void initialize();
-    public String walkerType();
-    
-    // Do we actually want to operate on the context?
-    boolean filter(LocusContext context, SAMRecord read);
-
-    // Map over the org.broadinstitute.sting.gatk.LocusContext
-    MapType map(LocusContext context, SAMRecord read);
-
-    // Given result of map function
-    ReduceType reduceInit();
-    ReduceType reduce(MapType value, ReduceType sum);
-
-    void onTraversalDone();
-}