moving some code around for better organizations, some fixes to the fields out of SSG

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1340 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -8,9 +8,8 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.ListUtils;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
-import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.genotype.calls.GenotypeCall;
-import org.broadinstitute.sting.utils.genotype.GenotypeCall;
+import org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall;
-import org.broadinstitute.sting.utils.genotype.SSGGenotypeCall;
 
 import java.io.File;
 import java.io.FileNotFoundException;

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

@@ -19,7 +19,7 @@ import org.broadinstitute.sting.utils.genotype.*;
 import java.io.File;
 
 @ReadFilters(ZeroMappingQualityReadFilter.class)
-public class SingleSampleGenotyper extends LocusWalker<SSGGenotypeCall, GenotypeWriter> {
+public class SingleSampleGenotyper extends LocusWalker<org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall, GenotypeWriter> {
     // Control output settings
     @Argument(fullName = "variants_out", shortName = "varout", doc = "File to which variants should be written", required = true) public File VARIANTS_FILE;
     @Argument(fullName = "metrics_out", shortName = "metout", doc = "File to which metrics should be written", required = false) public File METRICS_FILE = new File("/dev/stderr");
@@ -123,14 +123,14 @@ public class SingleSampleGenotyper extends LocusWalker<SSGGenotypeCall, Genotype
      *
      * @return an AlleleFrequencyEstimate object
      */
-    public SSGGenotypeCall map(RefMetaDataTracker tracker, char ref, LocusContext context) {
+    public org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         rationalizeSampleName(context.getReads().get(0));
         if (context.getLocation().getStart() == 73) {
             int stop = 1;
         }
         ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
         GenotypeLikelihoods G = callGenotype(tracker);
-        SSGGenotypeCall geno = (SSGGenotypeCall)G.callGenotypes(tracker, ref, pileup);
+        org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall geno = (org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall)G.callGenotypes(tracker, ref, pileup);
         if (geno != null) {
             metricsOut.nextPosition(geno, tracker);
         }
@@ -228,7 +228,7 @@ public class SingleSampleGenotyper extends LocusWalker<SSGGenotypeCall, Genotype
      *
      * @return an empty string
      */
-    public GenotypeWriter reduce(SSGGenotypeCall call, GenotypeWriter sum) {
+    public GenotypeWriter reduce(org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall call, GenotypeWriter sum) {
         if (call != null && call.isVariation()) {
             if (call.getConfidenceScore().getScore() > LOD_THRESHOLD)
                 sum.addGenotypeCall(call);

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

@@ -4,11 +4,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.refdata.rodGFF;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.genotype.calls.GenotypeCall;
-import org.broadinstitute.sting.utils.genotype.confidence.ConfidenceScore;
+import org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall;
-import org.broadinstitute.sting.utils.genotype.Genotype;
-import org.broadinstitute.sting.utils.genotype.GenotypeCall;
-import org.broadinstitute.sting.utils.genotype.SSGGenotypeCall;
 
 import java.io.File;
 import java.io.FileNotFoundException;

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

@@ -2,15 +2,21 @@ package org.broadinstitute.sting.playground.utils;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.genotype.*;
+import org.broadinstitute.sting.utils.ReadBackedPileup;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.genotype.BasicGenotype;
+import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.genotype.GenotypeGenerator;
+import org.broadinstitute.sting.utils.genotype.calls.GenotypeCall;
+import org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall;
 import org.broadinstitute.sting.utils.genotype.confidence.BayesianConfidenceScore;
 
 import static java.lang.Math.log10;
 import static java.lang.Math.pow;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
-import java.util.ArrayList;
 
 public class GenotypeLikelihoods implements GenotypeGenerator {
     // precalculate these for performance (pow/log10 is expensive!)

java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java

@@ -6,11 +6,10 @@ import org.broadinstitute.sting.utils.genotype.confidence.ConfidenceScore;
 
 
 /**
- * 
  * @author aaron
- * 
+ *         <p/>
  *         Class BasicGenotype
- *
+ *         <p/>
  *         A basic implementation of the genotype interface
  */
 public class BasicGenotype implements Genotype {
@@ -64,6 +63,7 @@ public class BasicGenotype implements Genotype {
 
     /**
      * get the confidence score
+     *
      * @return get the confidence score that we're based on
      */
     public ConfidenceScore getConfidenceScore() {
@@ -81,6 +81,7 @@ public class BasicGenotype implements Genotype {
 
     /**
      * get the ploidy
+     *
      * @return the ploidy value
      */
     public int getPloidy() {
@@ -117,6 +118,7 @@ public class BasicGenotype implements Genotype {
 
     /**
      * get the genotype's location
+     *
      * @return a GenomeLoc representing the location
      */
     public GenomeLoc getLocation() {
@@ -142,7 +144,7 @@ public class BasicGenotype implements Genotype {
      */
     @Override
     public boolean isVariant(char ref) {
-        String ret = Utils.dupString(ref,this.getPloidy());
+        String ret = Utils.dupString(ref, this.getPloidy());
         return !this.getBases().equals(ret);
     }
 
@@ -155,4 +157,13 @@ public class BasicGenotype implements Genotype {
     public Variant toVariant() {
         return null;
     }
+
+    /**
+     * set the confidence score
+     * @param confidenceScore
+     */
+    public void setConfidenceScore(ConfidenceScore confidenceScore) {
+        this.mConfidenceScore = confidenceScore;
+    }
+
 }

java/src/org/broadinstitute/sting/utils/genotype/ConfidenceScoreComparator.java

@@ -0,0 +1,20 @@
+package org.broadinstitute.sting.utils.genotype;
+
+import java.util.Comparator;
+
+
+/**
+ * 
+ * @author aaron 
+ * 
+ * Class ConfidenceScoreComparator
+ *
+ * A descriptions should go here. Blame aaron if it's missing.
+ */
+
+public class ConfidenceScoreComparator implements Comparator<Genotype> {
+    @Override
+    public int compare(Genotype genotype, Genotype genotype1) {
+        return genotype.getConfidenceScore().compareTo(genotype1.getConfidenceScore());
+    }
+}

java/src/org/broadinstitute/sting/utils/genotype/GenotypeGenerator.java

@@ -22,5 +22,5 @@ public interface GenotypeGenerator {
      * @param pileup a pileup of the reads, containing the reads and their offsets
      * @return a GenotypeLocus, containing each of the genotypes and their associated likelihood and posterior prob values
      */
-    public GenotypeCall callGenotypes(RefMetaDataTracker tracker, char ref, ReadBackedPileup pileup);
+    public org.broadinstitute.sting.utils.genotype.calls.GenotypeCall callGenotypes(RefMetaDataTracker tracker, char ref, ReadBackedPileup pileup);
 }

java/src/org/broadinstitute/sting/utils/genotype/GenotypeWriter.java

@@ -38,7 +38,7 @@ public interface GenotypeWriter {
      * Add a genotype, given a genotype locus
      * @param locus the locus to add
      */
-    public void addGenotypeCall(GenotypeCall locus);
+    public void addGenotypeCall(org.broadinstitute.sting.utils.genotype.calls.GenotypeCall locus);
 
     /**
      * add a no call to the genotype file, if supported.

java/src/org/broadinstitute/sting/utils/genotype/LexigraphicalComparator.java

@@ -0,0 +1,22 @@
+package org.broadinstitute.sting.utils.genotype;
+
+import java.util.Comparator;
+
+
+/**
+ * 
+ * @author aaron 
+ * 
+ * Class LexigraphicalComparator
+ *
+ * A descriptions should go here. Blame aaron if it's missing.
+ */
+
+public class LexigraphicalComparator implements Comparator<Genotype> {
+    private final Double EPSILON = 1.0e-15;
+
+    @Override
+    public int compare(Genotype genotype, Genotype genotype1) {
+        return genotype.getBases().compareTo(genotype1.getBases());
+    }
+}

java/src/org/broadinstitute/sting/utils/genotype/TabularLFWriter.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.utils.genotype;
 
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.genotype.calls.GenotypeCall;
 
 import java.io.File;
 import java.io.FileNotFoundException;

java/src/org/broadinstitute/sting/utils/genotype/calls/GenotypeCall.java

@@ -1,8 +1,8 @@
-package org.broadinstitute.sting.utils.genotype;
+package org.broadinstitute.sting.utils.genotype.calls;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.genotype.Genotype;
 
-import java.util.Comparator;
 import java.util.List;
 
 /**
@@ -51,19 +51,3 @@ public interface GenotypeCall extends Genotype {
     public List<Genotype> getLexigraphicallySortedGenotypes();
 
 }
-
-class LexigraphicalComparator implements Comparator<Genotype> {
-    private final Double EPSILON = 1.0e-15;
-
-    @Override
-    public int compare(Genotype genotype, Genotype genotype1) {
-        return genotype.getBases().compareTo(genotype1.getBases());
-    }
-}
-
-class ConfidenceScoreSort implements Comparator<Genotype> {
-    @Override
-    public int compare(Genotype genotype, Genotype genotype1) {
-        return genotype.getConfidenceScore().compareTo(genotype1.getConfidenceScore());
-    }
-}

java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java

@@ -1,14 +1,20 @@
-package org.broadinstitute.sting.utils.genotype;
+package org.broadinstitute.sting.utils.genotype.calls;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.ReadBackedPileup;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.genotype.confidence.ConfidenceScore;
+import org.broadinstitute.sting.utils.genotype.BasicGenotype;
+import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.genotype.LexigraphicalComparator;
+import org.broadinstitute.sting.utils.genotype.Variant;
 import org.broadinstitute.sting.utils.genotype.confidence.BayesianConfidenceScore;
+import org.broadinstitute.sting.utils.genotype.confidence.ConfidenceScore;
 
-import java.util.*;
+import java.util.ArrayList;
-
+import java.util.Collections;
-import net.sf.samtools.SAMRecord;
+import java.util.List;
+import java.util.TreeMap;
 
 
 /**
@@ -22,7 +28,7 @@ import net.sf.samtools.SAMRecord;
 public class SSGGenotypeCall implements GenotypeCall {
     // TODO: make SSG into a more robust Genotype call interface
     // our stored genotype locus
-    private final char mRefBase;
+    private final String mRefBase;
     private final int mPloidy;
     private final GenomeLoc mLoc;
     private TreeMap<Double, Genotype> mGenotypes = new TreeMap();
@@ -34,7 +40,7 @@ public class SSGGenotypeCall implements GenotypeCall {
     private double rmsMapping;
 
     public SSGGenotypeCall(char mRefBase, int mPloidy, GenomeLoc mLoc, List<Genotype> genotypes, double likelihoods[], ReadBackedPileup pileup) {
-        this.mRefBase = mRefBase;
+        this.mRefBase = String.valueOf(mRefBase).toUpperCase();
         this.mPloidy = mPloidy;
         this.mLoc = mLoc;
         if (genotypes.size() < 1) throw new IllegalArgumentException("Genotypes list size must be greater than 0");
@@ -56,7 +62,7 @@ public class SSGGenotypeCall implements GenotypeCall {
         mLikelihoods = likelihoods;
         index = 0;
         for (Genotype g : genotypes) {
-            ((BasicGenotype)g).mConfidenceScore = new BayesianConfidenceScore(Math.abs(likelihoods[index] - ref));
+            ((BasicGenotype)g).setConfidenceScore( new BayesianConfidenceScore(Math.abs(likelihoods[index] - ref)));
             mGenotypes.put(likelihoods[index],g);
             index++;            
         }
@@ -80,7 +86,7 @@ public class SSGGenotypeCall implements GenotypeCall {
      */
     @Override
     public char getReferencebase() {
-        return mRefBase;
+        return mRefBase.charAt(0);
     }
 
     /**
@@ -90,7 +96,7 @@ public class SSGGenotypeCall implements GenotypeCall {
      */
     @Override
     public boolean isVariation() {
-        return mGenotypes.get(mGenotypes.descendingKeySet().first()).isVariant(mRefBase);
+        return mGenotypes.get(mGenotypes.descendingKeySet().first()).isVariant(mRefBase.charAt(0));
     }
 
     /**

java/src/org/broadinstitute/sting/utils/genotype/geli/GeliAdapter.java

@@ -3,10 +3,10 @@ package org.broadinstitute.sting.utils.genotype.geli;
 import edu.mit.broad.picard.genotype.geli.GeliFileWriter;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMSequenceRecord;
-import org.broadinstitute.sting.utils.genotype.GenotypeCall;
 import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
 import org.broadinstitute.sting.utils.genotype.IndelLikelihood;
 import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
+import org.broadinstitute.sting.utils.genotype.calls.GenotypeCall;
 
 import java.io.File;
 
@@ -101,7 +101,7 @@ public class GeliAdapter implements GenotypeWriter {
      */
     @Override
     public void addGenotypeCall(GenotypeCall locus) {
-        //To change body of implemented methods use File | Settings | File Templates.
+        // TODO: add code here
     }
 
     /**

java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java

@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.utils.genotype.geli;
 
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.genotype.GenotypeCall;
+import org.broadinstitute.sting.utils.genotype.calls.GenotypeCall;
 import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
-import org.broadinstitute.sting.utils.genotype.SSGGenotypeCall;
+import org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -50,8 +50,8 @@ public class GeliTextWriter implements GenotypeWriter {
                                             call.getReadDepth(),
                                             -1,
 	                                        locus.getBases(),
-	                                        call.getConfidenceScore().getScore(),
+	                                        call.getBestRef(),
-	                                        locus.getConfidenceScore().getScore(),
+	                                        call.getBestNext(),
                                             call.getLikelihoods()[0],
                                             call.getLikelihoods()[1],
                                             call.getLikelihoods()[2],

java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java

@@ -4,7 +4,11 @@ import net.sf.samtools.SAMSequenceRecord;
 import net.sf.samtools.util.BinaryCodec;
 import net.sf.samtools.util.BlockCompressedOutputStream;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.genotype.*;
+import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
+import org.broadinstitute.sting.utils.genotype.IndelLikelihood;
+import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
+import org.broadinstitute.sting.utils.genotype.calls.GenotypeCall;
+import org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall;
 
 import java.io.DataOutputStream;
 import java.io.File;