Make the window and slide-by values command-line accessible, and standardize for every context. Move the test classes (which are abstract association context modules) into the proper directory.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5573 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java

@@ -86,8 +86,8 @@ public class ValidationReport extends VariantEvaluator implements StandardEval {
             for ( SiteStatus y : SiteStatus.values() )
                 nComp += getCounts(x, y);
 
-        if ( nComp != TP + FN + FP + TN )
-            throw new ReviewedStingException("BUG: nComp != TP + FN + FP + TN!");
+        if ( nComp != TP + FN + FP + TN + CompFiltered )
+            throw new ReviewedStingException("BUG: nComp != TP + FN + FP + TN + CompFiltered!");
 
         sensitivity = (100.0 * TP) / (TP + FN);
         PPV = (100.0 * TP) / (TP + FP);

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/AssociationContext.java

@@ -3,10 +3,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers.association;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 /**
  * Created by IntelliJ IDEA.
@@ -18,16 +15,23 @@ import java.util.Map;
 public abstract class AssociationContext<X,Y> {
 
     protected List<Map<Sample,Y>> window;
+    private final int size;
+    private final int slide;
 
     public AssociationContext() {
-        window = new ArrayList<Map<Sample,Y>>(getWindowSize());
+        this(0,0);
     }
 
-    // specifies size of window
-    public abstract int getWindowSize();
+    public AssociationContext(final int winSize, final int winSlide) {
+        window = new ArrayList<Map<Sample, Y>>(winSize);
+        size = winSize;
+        slide = winSlide;
+    }
 
-    // specifies how many bases to wait until next test
-    public abstract int slideByValue();
+    public AssociationContext(final RegionalAssociationWalker parent) {
+        this(parent.windowSize,parent.slideBy);
+        this.init(parent);
+    }
 
     // specifies whether to use previously seen reads
     public abstract boolean usePreviouslySeenReads();
@@ -66,12 +70,16 @@ public abstract class AssociationContext<X,Y> {
 
 
     public boolean isFull() {
-        return window.size() >= getWindowSize();
+        return window.size() >= size;
     }
 
     public void slide() {
-        ArrayList<Map<Sample,Y>> newWindow = new ArrayList<Map<Sample,Y>>((window.subList(slideByValue(),window.size())));
-        newWindow.ensureCapacity(getWindowSize());
+        ArrayList<Map<Sample,Y>> newWindow = new ArrayList<Map<Sample,Y>>((window.subList(slide,window.size())));
+        newWindow.ensureCapacity(size);
         window = newWindow;
     }
+
+    public int getWindowSize() {
+        return window.size();
+    }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationWalker.java

@@ -36,12 +36,17 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
     public String[] associationsToUse = null;
     @Argument(doc="Change output file to bedgraph format (s p q, not STAT: s P: p Q: q",shortName="bg",fullName="bedgraph",required=false)
     public boolean bedGraph = false;
+    @Argument(doc="Set the window size for associations to this value",shortName="w",fullName="window",required=false)
+    public int windowSize = 50;
+    @Argument(doc="Set the window sliding value for associations to this value",shortName="s",fullName="slide",required=false)
+    public int slideBy = 10;
 
     @Output
     @Multiplex(value=RegionalAssociationMultiplexer.class,arguments={"associationsToUse","bedGraph"})
     Map<AssociationContext,PrintStream> out;
 
     public void initialize() {
+        if ( windowSize < 1 ) { throw new UserException("Window size cannot be less than one."); }
 
         for ( Sample s : getSamples() ) {
             if ( s.getProperty("cohort") == null ) {
@@ -76,7 +81,6 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
             throw new StingException("Error in map reduce",e);
         }
         Map<AssociationContext,String> testsHere = rac.runTests(bedGraph);
-        // todo -- really awful shitty formatting
         if ( testsHere.size() > 0 ) {
             for ( Map.Entry<AssociationContext,String> result : testsHere.entrySet() ) {
                 out.get(result.getKey().getClass()).printf("%s%n",result.getValue());
@@ -88,18 +92,15 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
     public Set<AssociationContext> getAssociations() {
         List<Class<? extends AssociationContext>> contexts = new PluginManager<AssociationContext>(AssociationContext.class).getPlugins();
 
-
-
         if ( associationsToUse.length > 0 && associationsToUse[0].equals("ALL") ) {
             HashSet<AssociationContext> allAssoc =  new HashSet<AssociationContext>(contexts.size());
             for ( Class<? extends AssociationContext> clazz : contexts ) {
                 AssociationContext context;
                 try {
-                    context = clazz.newInstance();
+                    context = clazz.getConstructor(new Class[] {RegionalAssociationWalker.class}).newInstance(new Object[] {this});
                 } catch (Exception e ) {
                     throw new StingException("The class "+clazz.getSimpleName()+" could not be instantiated",e);
                 }
-                context.init(this);
                 allAssoc.add(context);
             }
             return allAssoc;
@@ -115,11 +116,10 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
         for ( String s : associationsToUse ) {
             AssociationContext context;
             try {
-                context = classNameToClass.get(s).newInstance();
+                context = classNameToClass.get(s).getConstructor(new Class[]{RegionalAssociationWalker.class}).newInstance(new Object[] {this});
             } catch ( Exception e ) {
                 throw new StingException("The class "+s+" could not be instantiated.",e);
             }
-            context.init(this);
             validAssociations.add(context);
         }
         return validAssociations;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/BaseQualityScore.java

@@ -1,7 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.TStatistic;
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.UStatistic;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -26,7 +24,5 @@ public class BaseQualityScore extends TStatistic {
         return (Collection) baseQuals;
     }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return true; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/CaseControl.java

@@ -1,4 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
+
 
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.oneoffprojects.walkers.association.AssociationContext;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/FisherExact.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
 /**
  * Created by IntelliJ IDEA.

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/InsertSizeDistribution.java

@@ -1,7 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.TStatistic;
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.UStatistic;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -12,9 +10,8 @@ import java.util.List;
 /**
  * @author chartl
  */
-public class InsertSizeDistribution extends TStatistic {
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
+public class InsertSizeDistribution extends UStatistic {
+
     public boolean usePreviouslySeenReads() { return false; }
 
     public Collection<Number> map(ReadBackedPileup pileup) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MappingQuality0.java

@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.ZStatistic;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -26,8 +25,6 @@ public class MappingQuality0 extends ZStatistic {
         return new Pair<Number,Number>(mq0,total);
     }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateMappingQuality.java

@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.UStatistic;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -27,7 +26,5 @@ public class MateMappingQuality extends UStatistic {
         return (Collection) mateMapQ;
     }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateOtherContig.java

@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.ZStatistic;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -14,8 +13,6 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
  */
 public class MateOtherContig extends ZStatistic {
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 
     public Pair<Number,Number> map(ReadBackedPileup pileup) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateSameStrand.java

@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.ZStatistic;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -29,7 +28,5 @@ public class MateSameStrand extends ZStatistic {
         return new Pair<Number,Number>(mateSameStrand,numPairs);
     }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateUnmapped.java

@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.ZStatistic;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -29,7 +28,5 @@ public class MateUnmapped extends ZStatistic  {
         return new Pair<Number,Number>(numPairUnmapped,numMatedReads);
     }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MismatchRate.java

@@ -1,9 +1,8 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.oneoffprojects.walkers.association.MapExtender;
 import org.broadinstitute.sting.oneoffprojects.walkers.association.RegionalAssociationWalker;
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.UStatistic;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
@@ -85,7 +84,5 @@ public class MismatchRate extends UStatistic {
     // note: this is to satisfy the interface, and is never called due to override
     public Collection<Number> map(ReadBackedPileup pileup) { return null; }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return true; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ProperPairs.java

@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.ZStatistic;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -27,7 +26,5 @@ public class ProperPairs extends ZStatistic {
         return new Pair<Number,Number>(numPropPair,numReads);
     }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ReadClipping.java

@@ -1,8 +1,7 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.TStatistic;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -33,7 +32,5 @@ public class ReadClipping extends TStatistic {
         return (Collection) clipping;
     }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ReadIndels.java

@@ -1,9 +1,7 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.TStatistic;
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.UStatistic;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -33,7 +31,5 @@ public class ReadIndels extends UStatistic {
         return (Collection) indelElements;
     }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ReadMappingQuality.java

@@ -1,7 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.TStatistic;
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.UStatistic;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -26,7 +24,5 @@ public class ReadMappingQuality extends TStatistic {
         return (Collection) mapQuals;
     }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return false; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ReferenceMismatches.java

@@ -1,8 +1,7 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.oneoffprojects.walkers.association.MapExtender;
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.ZStatistic;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -42,7 +41,5 @@ public class ReferenceMismatches extends ZStatistic {
         return new Pair<Number,Number>(nonref,total);
     }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return true; }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/SampleDepth.java

@@ -1,15 +1,10 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.oneoffprojects.walkers.association.MapExtender;
 import org.broadinstitute.sting.oneoffprojects.walkers.association.RegionalAssociationWalker;
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.TStatistic;
-import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.UStatistic;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.*;
@@ -75,8 +70,6 @@ public class SampleDepth extends UStatistic {
     // note: this is to satisfy the interface, and is never called due to override
     public Collection<Number> map(ReadBackedPileup pileup) { return null; }
 
-    public int getWindowSize() { return 100; }
-    public int slideByValue() { return 10; }
     public boolean usePreviouslySeenReads() { return true; }
 
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/TStatistic.java

@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.ArrayList;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/UStatistic.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/ZStatistic.java

@@ -1,13 +1,8 @@
-package org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol;
+package org.broadinstitute.sting.oneoffprojects.walkers.association.modules.casecontrol;
 
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Set;
-
 /**
  * Created by IntelliJ IDEA.
  * User: chartl