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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
This commit is contained in:
aaron 2009-07-30 15:09:43 +00:00
parent 4366ce16e0
commit 4033c718d2
15 changed files with 111 additions and 61 deletions
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5
java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java
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@ -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.GenotypeCall;
import org.broadinstitute.sting.utils.genotype.SSGGenotypeCall;
import org.broadinstitute.sting.utils.genotype.calls.GenotypeCall;
import org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall;
import java.io.File;
import java.io.FileNotFoundException;

8
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
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@ -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);

7
java/src/org/broadinstitute/sting/playground/utils/AlleleMetrics.java
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@ -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.confidence.ConfidenceScore;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.GenotypeCall;
import org.broadinstitute.sting.utils.genotype.SSGGenotypeCall;
import org.broadinstitute.sting.utils.genotype.calls.GenotypeCall;
import org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall;
import java.io.File;
import java.io.FileNotFoundException;

12
java/src/org/broadinstitute/sting/playground/utils/GenotypeLikelihoods.java
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@ -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.genotype.*;
import org.broadinstitute.sting.utils.MathUtils;
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!)

29
java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java
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@ -6,12 +6,11 @@ import org.broadinstitute.sting.utils.genotype.confidence.ConfidenceScore;
/**
*
* @author aaron
*
* Class BasicGenotype
*
* A basic implementation of the genotype interface
* @author aaron
* <p/>
* Class BasicGenotype
* <p/>
* A basic implementation of the genotype interface
*/
public class BasicGenotype implements Genotype {
@ -30,7 +29,7 @@ public class BasicGenotype implements Genotype {
/**
* construct a genotypeLikelihood, given the bases, the confidence score, and the ploidy
*
* @param loc the location of the genotype
* @param loc the location of the genotype
* @param bases the bases that make up this genotype
* @param ploidy the ploidy of this genotype
* @param score the confidence score
@ -49,7 +48,7 @@ public class BasicGenotype implements Genotype {
* construct a genotypeLikelihood, given the bases and the confidence score, and assume the
* ploidy is 2.
*
* @param loc the location of the genotype
* @param loc the location of the genotype
* @param bases the bases that make up this genotype
* @param score the confidence score
*/
@ -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;
}
}

20
java/src/org/broadinstitute/sting/utils/genotype/ConfidenceScoreComparator.java 100644
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@ -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());
}
}

2
java/src/org/broadinstitute/sting/utils/genotype/GenotypeGenerator.java
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@ -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);
}

2
java/src/org/broadinstitute/sting/utils/genotype/GenotypeWriter.java
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@ -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.

22
java/src/org/broadinstitute/sting/utils/genotype/LexigraphicalComparator.java 100644
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@ -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());
}
}

1
java/src/org/broadinstitute/sting/utils/genotype/TabularLFWriter.java
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@ -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;

20
java/src/org/broadinstitute/sting/utils/genotype/GenotypeCall.java → java/src/org/broadinstitute/sting/utils/genotype/calls/GenotypeCall.java
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@ -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());
}
}

26
java/src/org/broadinstitute/sting/utils/genotype/SSGGenotypeCall.java → java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java
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@ -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 net.sf.samtools.SAMRecord;
import java.util.ArrayList;
import java.util.Collections;
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));
}
/**

4
java/src/org/broadinstitute/sting/utils/genotype/geli/GeliAdapter.java
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@ -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
}
/**

8
java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java
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@ -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(),
locus.getConfidenceScore().getScore(),
call.getBestRef(),
call.getBestNext(),
call.getLikelihoods()[0],
call.getLikelihoods()[1],
call.getLikelihoods()[2],

6
java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
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@ -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;