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Major refactoring of association testing framework. New modules are now beyond trivial to implement. One hurdle remains which is how to deal with statistics that ought to be sample-normalized (e.g. depth, insert-size [when multiple libraries are used], and possibly others). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5366 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-03-03 14:27:16 +00:00
parent 5d4bbf41fb
commit ef38fd1e0e
18 changed files with 358 additions and 312 deletions
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72
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/AssociationContext.java
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@ -1,42 +1,74 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association;
import java.lang.reflect.InvocationTargetException;
import java.util.*;
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;
/**
* @Author chartl
* @Date 2011-02-23
* A general context for windowed association
* Created by IntelliJ IDEA.
* User: chartl
* Date: 3/2/11
* Time: 11:58 AM
* To change this template use File | Settings | File Templates.
*/
public abstract class AssociationContext<X extends AssociationContextAtom> {
protected Class<? extends AssociationContextAtom> clazz;
protected List<X> window;
public abstract class AssociationContext<X> {
public AssociationContext( Class<X> zclaz ) {
window = new ArrayList<X>(getWindowSize());
clazz = zclaz;
protected List<Map<Sample,Object>> window;
public AssociationContext() {
window = new ArrayList<Map<Sample,Object>>(getWindowSize());
}
public X map(MapExtender e) throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException, ClassCastException {
return (X) clazz.getConstructor(new Class[] {MapExtender.class}).newInstance(new Object[] {e});
}
// specifies size of window
public abstract int getWindowSize();
// specifies how many bases to wait until next test
public abstract int slideByValue();
// specifies whether to use previously seen reads
public abstract boolean usePreviouslySeenReads();
// specifies the map from a sample's pileup to the data we want to test
public abstract Object map(ReadBackedPileup rbp);
// specifies how to take the per-sample data and reduce them into testable pairs
public abstract Map<?,X> reduce(List<Map<Sample,X>> win);
// do we filter the current location (e.g. omit from window)
public boolean filter(MapExtender m) { return true; }
public void reduce(X context) {
window.add(context);
public Map<Sample,Object> mapLocus(MapExtender extender) {
Map<Sample,ReadBackedPileup> pileups;
if ( ! usePreviouslySeenReads() ) {
pileups = extender.getReadFilteredPileup();
} else {
pileups = extender.getFullPileup();
}
Map<Sample,Object> maps = new HashMap<Sample,Object>(pileups.size());
for ( Map.Entry<Sample,ReadBackedPileup> samPileup : pileups.entrySet() ) {
maps.put(samPileup.getKey(),map(samPileup.getValue()));
}
return maps;
}
public void addData(Map<Sample,Object> sampleData) {
window.add(sampleData);
}
public abstract int getWindowSize();
public abstract int slideByValue();
public boolean isFull() {
return window.size() >= getWindowSize();
}
public void slide() {
ArrayList<X> newWindow = new ArrayList<X>((window.subList(slideByValue(),window.size())));
ArrayList<Map<Sample,Object>> newWindow = new ArrayList<Map<Sample,Object>>((window.subList(slideByValue(),window.size())));
newWindow.ensureCapacity(getWindowSize());
window = newWindow;
}
}
}

13
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/AssociationContextAtom.java
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@ -1,13 +0,0 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association;
/**
* @Author chartl
* @Date 2011-02-23
* general class for calculating base data for generalized association tests
*/
public abstract class AssociationContextAtom {
public AssociationContextAtom(MapExtender e) {
}
}

19
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/AssociationTestRunner.java
View File

@ -5,7 +5,8 @@ import java.util.List;
import cern.jet.random.Normal;
import cern.jet.random.StudentT;
import org.broadinstitute.sting.oneoffprojects.walkers.association.interfaces.*;
import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.*;
import org.broadinstitute.sting.utils.MathUtils;
/**
* Created by IntelliJ IDEA.
@ -34,17 +35,19 @@ public class AssociationTestRunner {
return results;
}
public static String runStudentT(TStatistic context) {
double t = context.getTStatistic();
StudentT studentT = new StudentT(context.getDegreesOfFreedom(),null);
public static String runStudentT(TStatistic context) { /*
StudentT studentT = new StudentT(dfnum/dfdenom,null);
double p = t < 0 ? 2*studentT.cdf(t) : 2*(1-studentT.cdf(t));
return String.format("T: %.2f\tP: %.2e",t,p);
return String.format("T: %.2f\tP: %.2e",t,p);*/
return null;
}
public static String runZ(ZStatistic context) {
double z = context.getZStatistic();
public static String runZ(ZStatistic context) { /*
double z = num/Math.sqrt(se);
double p = z < 0 ? 2*standardNormal.cdf(z) : 2*(1-standardNormal.cdf(z));
return String.format("Z: %.2f\tP: %.2e",z,p);
return String.format("Z: %.2f\tP: %.2e",z,p);*/
return null;
}
public static String runFisherExact(AssociationContext context) {

45
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/MapExtender.java
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@ -1,11 +1,16 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import java.util.Map;
import java.util.*;
/**
* @Author chartl
@ -13,9 +18,12 @@ import java.util.Map;
* Holds multiple map contexts for use in the regional association walker
*/
public class MapExtender {
static StratifiedAlignmentContext.StratifiedContextType TYPE = StratifiedAlignmentContext.StratifiedContextType.COMPLETE;
// hold on to these -- atoms may want access to the tracker or other context types
private MapHolder previous = null;
private MapHolder current = null;
private Map<Sample,ReadBackedPileup> fullPileup = null;
private Map<Sample,ReadBackedPileup> readFilteredPileup = null;
public MapExtender() {
// no need to do anything
@ -24,8 +32,41 @@ public class MapExtender {
public void set(MapHolder holder) {
previous = current;
current = holder;
Map<Sample,ReadBackedPileup> prevPileup = fullPileup;
fullPileup = new HashMap<Sample,ReadBackedPileup>();
readFilteredPileup = new HashMap<Sample,ReadBackedPileup>();
if ( current != null ) {
for ( Map.Entry<Sample,StratifiedAlignmentContext> sac : current.getContext().entrySet() ) {
AlignmentContext context = sac.getValue().getContext(TYPE);
if ( context.hasBasePileup() ) {
fullPileup.put(sac.getKey(),context.getBasePileup());
} else if ( context.hasExtendedEventPileup() ) {
fullPileup.put(sac.getKey(),context.getExtendedEventPileup());
}
if ( prevPileup != null ) {
List<PileupElement> filtElems = new ArrayList<PileupElement>(fullPileup.get(sac.getKey()).size());
Set<SAMRecord> seenReads = prevPileup.containsKey(sac.getKey()) ? new HashSet<SAMRecord>(prevPileup.get(sac.getKey()).getReads()) : new HashSet<SAMRecord>(0);
for ( PileupElement e : fullPileup.get(sac.getKey()) ) {
if ( ! seenReads.contains(e.getRead()) ) {
filtElems.add(e);
}
}
readFilteredPileup.put(sac.getKey(),new ReadBackedPileupImpl(current.getRef().getLocus(),filtElems));
} else {
readFilteredPileup = fullPileup;
}
}
}
}
public Map<Sample,ReadBackedPileup> getFullPileup() { return fullPileup; }
public Map<Sample,ReadBackedPileup> getReadFilteredPileup(){ return readFilteredPileup; }
public Map<Sample,StratifiedAlignmentContext> getPreviousContext() {
return previous != null ? previous.getContext() : null;
}

5
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationHandler.java
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@ -2,7 +2,6 @@ package org.broadinstitute.sting.oneoffprojects.walkers.association;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.lang.reflect.InvocationTargetException;
import java.util.*;
/**
@ -31,10 +30,10 @@ public class RegionalAssociationHandler {
* @reduce: (List<AssociationContext>,AssociationContext) --> List<AssociationContextAtom>
* @implementation: just append
*/
public void runMapReduce() throws NoSuchMethodException, IllegalAccessException, InstantiationException, InvocationTargetException {
public void runMapReduce() {
for ( AssociationContext w : associations ) {
if ( w.filter(maps) ) {
w.reduce(w.map(maps));
w.addData(w.mapLocus(maps));
}
}
}

7
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationWalker.java
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@ -7,8 +7,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.oneoffprojects.walkers.association.modules.LowMappingQuality;
import org.broadinstitute.sting.oneoffprojects.walkers.association.modules.LowMappingQualityAtom;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -59,11 +57,8 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
}
private AssociationContext stringToAssociationContext(String s) {
if ( s.equals("LowMappingQuality") ) {
return new LowMappingQuality();
}
throw new UserException(String.format("AssociationContext type %s not found.",s));
throw new UserException(String.format("AssociationContextOld type %s not found.",s));
}
private Set<AssociationContext> getAssociations() {

15
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/interfaces/TStatistic.java
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@ -1,15 +0,0 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.interfaces;
import org.broadinstitute.sting.utils.collections.Pair;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: Feb 24, 2011
* Time: 12:58:16 PM
* To change this template use File | Settings | File Templates.
*/
public interface TStatistic {
public abstract double getTStatistic();
public abstract double getDegreesOfFreedom();
}

12
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/interfaces/ZStatistic.java
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@ -1,12 +0,0 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.interfaces;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: Feb 24, 2011
* Time: 12:58:38 PM
* To change this template use File | Settings | File Templates.
*/
public interface ZStatistic {
public abstract double getZStatistic();
}

28
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/InsertSizeDistribution.java 100755
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@ -0,0 +1,28 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
import org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol.TStatistic;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
/**
* @author chartl
*/
public class InsertSizeDistribution extends TStatistic {
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return false; }
public Collection<Number> map(ReadBackedPileup pileup) {
List<Integer> insertSizes = new ArrayList<Integer>(pileup.size());
for ( PileupElement e : pileup ) {
insertSizes.add(e.getRead().getInferredInsertSize());
}
return (Collection) insertSizes;
}
}

89
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/LowMappingQuality.java
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@ -1,89 +0,0 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.oneoffprojects.walkers.association.AssociationContext;
import org.broadinstitute.sting.oneoffprojects.walkers.association.AssociationContextAtom;
import org.broadinstitute.sting.oneoffprojects.walkers.association.interfaces.TStatistic;
import org.broadinstitute.sting.oneoffprojects.walkers.association.interfaces.ZStatistic;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import java.util.*;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: Feb 24, 2011
* Time: 1:49:37 PM
* To change this template use File | Settings | File Templates.
*/
public class LowMappingQuality extends AssociationContext<LowMappingQualityAtom> implements ZStatistic, TStatistic {
private double df = -1;
public LowMappingQuality(Class<LowMappingQualityAtom> atomClass ) {
super(atomClass);
}
public LowMappingQuality() {
this(LowMappingQualityAtom.class);
}
public int getWindowSize() { return 20; }
public int slideByValue() { return 5; }
public double getZStatistic() {
int case_low= 0;
int case_tot = 0;
int ctrl_low = 0;
int ctrl_tot = 0;
for ( LowMappingQualityAtom atom : window ) {
Map<String, Pair<Integer,Integer>> ccc = atom.getCaseControlCounts();
case_low += ccc.get("case").first;
case_tot += ccc.get("case").second;
ctrl_low += ccc.get("control").first;
ctrl_tot += ccc.get("control").second;
}
double p_case = ( (double) case_low)/case_tot;
double p_ctrl = ((double) ctrl_low)/ctrl_tot;
double p_pool = ( (double) case_low + (double) ctrl_low )/(case_tot+ctrl_tot);
double SE = Math.sqrt( p_pool*(1-p_pool)*( 1/((double)ctrl_tot) + 1/((double)case_tot) ));
return (p_case - p_ctrl)/SE;
}
public double getTStatistic() {
// todo -- running average is unnecessary and inefficient here, but was quick to write
MathUtils.RunningAverage cases = new MathUtils.RunningAverage();
MathUtils.RunningAverage controls = new MathUtils.RunningAverage();
Set<Sample> caseSamples = new HashSet<Sample>();
Set<Sample> controlSamples = new HashSet<Sample>();
for ( LowMappingQualityAtom atom : window ) {
Map<String,List<Integer>> caseControlQuals = atom.getCaseControlMappingQuals();
cases.addAll((Collection) caseControlQuals.get("case"));
controls.addAll((Collection) caseControlQuals.get("control"));
for ( Sample s : atom.getSamples() ) {
if ( s.getProperty("cohort").equals("case") ) {
caseSamples.add(s);
}
if ( s.getProperty("cohort").equals("control")) {
controlSamples.add(s);
}
}
}
double a = cases.var()/caseSamples.size();
double b = controls.var()/controlSamples.size();
df = ( a + b )/( a*a/(caseSamples.size()-1) + b*b/(controlSamples.size()-1));
return ( cases.mean() - controls.mean() )/Math.sqrt( (cases.var()/caseSamples.size()) + (controls.var()/controlSamples.size()));
}
// todo -- this is super hacky
public double getDegreesOfFreedom() {
if ( df < 0 ) {
getTStatistic();
}
double holder = df;
df = -1;
return holder;
}
}

143
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/LowMappingQualityAtom.java
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@ -1,143 +0,0 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.oneoffprojects.walkers.association.AssociationContextAtom;
import org.broadinstitute.sting.oneoffprojects.walkers.association.MapExtender;
import org.broadinstitute.sting.oneoffprojects.walkers.association.MapHolder;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import java.util.*;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: Feb 24, 2011
* Time: 1:49:55 PM
* To change this template use File | Settings | File Templates.
*/
public class LowMappingQualityAtom extends AssociationContextAtom {
private static int LOW_THRESH = 5;
private static StratifiedAlignmentContext.StratifiedContextType TYPE = StratifiedAlignmentContext.StratifiedContextType.COMPLETE;
protected Map<Sample, Pair<Integer,Integer>> stratifiedCounts;
protected Map<Sample,List<Integer>> mappingQualities;
public LowMappingQualityAtom(MapExtender e) {
super(e);
stratifiedCounts = new HashMap<Sample,Pair<Integer,Integer>>();
mappingQualities = new HashMap<Sample,List<Integer>>();
for ( Sample s : e.getContext().keySet() ) {
makeCounts(s,e.getPreviousContext(),e.getContext());
}
}
public void makeCounts( Sample sample, Map<Sample, StratifiedAlignmentContext> prev, Map<Sample,StratifiedAlignmentContext> cur ) {
int low = 0;
int tot = 0;
if ( cur != null && cur.get(sample) != null && cur.get(sample).getContext(TYPE) != null) {
HashSet<String> rnames;
List<Integer> mapQuals = new ArrayList<Integer>(cur.size());
if ( prev != null && prev.get(sample) != null && prev.get(sample).getContext(TYPE) != null) {
rnames = new HashSet<String>(prev.get(sample).getContext(TYPE).size());
if ( prev.get(sample).getContext(TYPE).hasBasePileup()) {
for ( PileupElement e : prev.get(sample).getContext(TYPE).getBasePileup() ) {
rnames.add(e.getRead().getReadName());
}
}
if ( prev.get(sample).getContext(TYPE).hasExtendedEventPileup()) {
for ( PileupElement e : prev.get(sample).getContext(TYPE).getExtendedEventPileup() ) {
rnames.add(e.getRead().getReadName());
}
}
} else {
rnames = new HashSet<String>(0);
}
if ( cur.get(sample).getContext(TYPE).hasBasePileup()) {
for ( PileupElement e : cur.get(sample).getContext(TYPE).getBasePileup() ) {
if ( ! rnames.contains(e.getRead().getReadName()) ) {
++tot;
if ( e.getMappingQual() < LOW_THRESH ) {
++low;
}
mapQuals.add(e.getMappingQual());
}
}
}
if ( cur.get(sample).getContext(TYPE).hasExtendedEventPileup()) {
for ( PileupElement e : cur.get(sample).getContext(TYPE).getExtendedEventPileup() ) {
if ( ! rnames.contains(e.getRead().getReadName()) ) {
++tot;
if ( e.getMappingQual() < LOW_THRESH ) {
++low;
}
mapQuals.add(e.getMappingQual());
}
}
}
stratifiedCounts.put(sample,new Pair<Integer,Integer>(low,tot));
mappingQualities.put(sample,mapQuals);
}
}
public Map<Sample,Pair<Integer,Integer>> getCounts() {
return stratifiedCounts;
}
public Map<String,Pair<Integer,Integer>> getCaseControlCounts() {
Pair<Integer,Integer> cases = new Pair<Integer,Integer>(0,0);
Pair<Integer,Integer> controls = new Pair<Integer,Integer>(0,0);
for ( Map.Entry<Sample,Pair<Integer,Integer>> e : stratifiedCounts.entrySet() ) {
if ( e.getKey().getProperty("cohort").equals("case") ) {
cases.first += e.getValue().first;
cases.second += e.getValue().second;
}
if ( e.getKey().getProperty("cohort").equals("control") ) {
controls.first += e.getValue().first;
controls.second += e.getValue().second;
}
}
Map<String,Pair<Integer,Integer>> caseControlCounts= new HashMap<String,Pair<Integer,Integer>>(2);
caseControlCounts.put("case",cases);
caseControlCounts.put("control",controls);
return caseControlCounts;
}
public Map<String,List<Integer>> getCaseControlMappingQuals() {
int caseSize = 0;
int controlSize = 0;
for ( Map.Entry<Sample,List<Integer>> v : mappingQualities.entrySet() ) {
if ( v.getKey().getProperty("cohort").equals("case") ) {
caseSize += v.getValue().size();
}
if ( v.getKey().getProperty("cohort").equals("control") ) {
controlSize += v.getValue().size();
}
}
List<Integer> caseQuals = new ArrayList<Integer>(caseSize);
List<Integer> controlQuals = new ArrayList<Integer>(controlSize);
for ( Map.Entry<Sample,List<Integer>> v : mappingQualities.entrySet() ) {
if ( v.getKey().getProperty("cohort").equals("case") ) {
caseQuals.addAll(v.getValue());
}
if ( v.getKey().getProperty("cohort").equals("control")) {
controlQuals.addAll(v.getValue());
}
}
Map<String,List<Integer>> caseControlQuals = new HashMap<String,List<Integer>>(2);
caseControlQuals.put("case",caseQuals);
caseControlQuals.put("control",controlQuals);
return caseControlQuals;
}
public Set<Sample> getSamples() {
return stratifiedCounts.keySet();
}
}

36
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MateOtherContig.java 100755
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@ -0,0 +1,36 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
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;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: 3/1/11
* Time: 3:00 PM
* To change this template use File | Settings | File Templates.
*/
public class MateOtherContig extends ZStatistic {
public int getWindowSize() { return 50; }
public int slideByValue() { return 25; }
public boolean usePreviouslySeenReads() { return false; }
public Pair<Number,Number> map(ReadBackedPileup pileup) {
int tot = 0;
int otherCon = 0;
for ( PileupElement e : pileup ) {
if ( e.getRead().getReadPairedFlag() ) {
++tot;
if ( ! e.getRead().getMateReferenceIndex().equals(e.getRead().getReferenceIndex()) ) {
++otherCon;
}
}
}
return new Pair<Number,Number>(tot,otherCon);
}
}

35
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MateUnmapped.java 100755
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@ -0,0 +1,35 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.modules;
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;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: 3/2/11
* Time: 2:09 PM
* To change this template use File | Settings | File Templates.
*/
public class MateUnmapped extends ZStatistic {
public Pair<Number,Number> map(ReadBackedPileup pileup) {
int numMatedReads = 0;
int numPairUnmapped = 0;
for (PileupElement e : pileup ) {
if ( e.getRead().getProperPairFlag() ) {
++numMatedReads;
if ( e.getRead().getMateUnmappedFlag() ) {
++numPairUnmapped;
}
}
}
return new Pair<Number,Number>(numMatedReads,numPairUnmapped);
}
public int getWindowSize() { return 100; }
public int slideByValue() { return 25; }
public boolean usePreviouslySeenReads() { return false; }
}

50
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/statistics/casecontrol/CaseControl.java 100755
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@ -0,0 +1,50 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol;
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.oneoffprojects.walkers.association.AssociationContext;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Created by IntelliJ IDEA.
* @author chartl
*/
public abstract class CaseControl<X> extends AssociationContext<X> {
public Map<Cohort,X> reduce(List<Map<Sample,X>> window) {
X accumCase = null;
X accumControl = null;
for ( Map<Sample,X> sampleXMap : window ) {
for ( Map.Entry<Sample,X> entry : sampleXMap.entrySet() ) {
if ( entry.getKey().getProperty("cohort").equals("case") ) {
accum(accumCase, entry.getValue());
} else if ( entry.getKey().getProperty("cohort").equals("control") ) {
accum(accumControl,entry.getValue());
}
}
}
Map<Cohort,X> cohortMap = new HashMap<Cohort,X>(2);
cohortMap.put(Cohort.CASE,accumCase);
cohortMap.put(Cohort.CONTROL,accumControl);
return cohortMap;
}
protected X accum(X left, X right) {
if ( left == null ) {
return right;
}
if ( right == null ) {
return left;
}
return add(left,right);
}
public abstract X map(ReadBackedPileup rbp);
public abstract X add(X left, X right);
public enum Cohort { CASE,CONTROL }
}

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/interfaces/FisherExact.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/statistics/casecontrol/FisherExact.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.interfaces;
package org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol;
/**
* Created by IntelliJ IDEA.

37
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/statistics/casecontrol/TStatistic.java 100755
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@ -0,0 +1,37 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.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
* Date: Feb 24, 2011
* Time: 12:58:16 PM
* To change this template use File | Settings | File Templates.
*/
public abstract class TStatistic extends CaseControl<Collection<Number>> {
public abstract Collection<Number> map(ReadBackedPileup rbp );
public Collection<Number> add(Collection<Number> left, Collection<Number> right) {
if ( left instanceof List) {
((List) left).addAll(right);
return left;
} else if ( left instanceof Set ) {
((Set) left).addAll(right);
return left;
} else {
List<Number> newList = new ArrayList<Number>(left.size()+right.size());
newList.addAll(left);
newList.addAll(right);
return newList;
}
}
}

36
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/statistics/casecontrol/UStatistic.java 100755
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@ -0,0 +1,36 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.casecontrol;
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
* Date: 3/2/11
* Time: 1:53 PM
* To change this template use File | Settings | File Templates.
*/
public abstract class UStatistic extends CaseControl<Collection<Number>> {
public abstract Collection<Number> map(ReadBackedPileup rbp );
public Collection<Number> add(Collection<Number> left, Collection<Number> right) {
if ( left instanceof List) {
((List) left).addAll(right);
return left;
} else if ( left instanceof Set) {
((Set) left).addAll(right);
return left;
} else {
List<Number> newList = new ArrayList<Number>(left.size()+right.size());
newList.addAll(left);
newList.addAll(right);
return newList;
}
}
}

26
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/statistics/casecontrol/ZStatistic.java 100755
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@ -0,0 +1,26 @@
package org.broadinstitute.sting.oneoffprojects.walkers.association.statistics.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
* Date: Feb 24, 2011
* Time: 12:58:38 PM
* To change this template use File | Settings | File Templates.
*/
public abstract class ZStatistic extends CaseControl<Pair<Number,Number>> {
public abstract Pair<Number,Number> map(ReadBackedPileup rbp );
public Pair<Number,Number> add(Pair<Number,Number> left, Pair<Number,Number> right) {
return new Pair<Number,Number>(left.first.doubleValue()+right.first.doubleValue(),
left.second.doubleValue()+right.second.doubleValue());
}
}