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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Guillermo del Angel 2011-09-24 21:20:11 -04:00
parent 4707ab4a7d 466ffa3665
commit 3eef800889
16 changed files with 130 additions and 21 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -34,12 +34,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.genotype.Haplotype;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;

4
public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java → public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.genotype;
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.utils.BaseUtils;
@ -34,7 +34,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
* Time: 6:46:09 PM
* To change this template use File | Settings | File Templates.
*/
public enum DiploidGenotype {
enum DiploidGenotype {
AA ('A', 'A'),
AC ('A', 'C'),
AG ('A', 'G'),

1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java
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@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
/**
* Created by IntelliJ IDEA.

1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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@ -30,7 +30,6 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.pileup.FragmentPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypePriors.java
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@ -26,7 +26,6 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import java.util.Arrays;

7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -34,10 +34,9 @@ import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.genotype.Haplotype;
import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
@ -396,8 +395,8 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
System.out.format("hsize: %d eventLength: %d refSize: %d, locStart: %d numpr: %d\n",hsize,eventLength,
(int)ref.getWindow().size(), loc.getStart(), numPrefBases);
//System.out.println(eventLength);
haplotypeMap = Haplotype.makeHaplotypeListFromAlleles( alleleList, loc.getStart(),
ref, hsize, numPrefBases);
haplotypeMap = Haplotype.makeHaplotypeListFromAlleles(alleleList, loc.getStart(),
ref, hsize, numPrefBases);
// For each sample, get genotype likelihoods based on pileup
// compute prior likelihoods on haplotypes, and initialize haplotype likelihood matrix with them.

1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -34,7 +34,6 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;

17
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -544,6 +544,21 @@ public class UnifiedGenotyperEngine {
AFs[i] = AlleleFrequencyCalculationModel.VALUE_NOT_CALCULATED;
}
private final static double[] binomialProbabilityDepthCache = new double[10000];
static {
for ( int i = 1; i < binomialProbabilityDepthCache.length; i++ ) {
binomialProbabilityDepthCache[i] = MathUtils.binomialProbability(0, i, 0.5);
}
}
private final double getRefBinomialProb(final int depth) {
if ( depth < binomialProbabilityDepthCache.length )
return binomialProbabilityDepthCache[depth];
else
return MathUtils.binomialProbability(0, depth, 0.5);
}
private VariantCallContext estimateReferenceConfidence(VariantContext vc, Map<String, AlignmentContext> contexts, double theta, boolean ignoreCoveredSamples, double initialPofRef) {
if ( contexts == null )
return null;
@ -567,7 +582,7 @@ public class UnifiedGenotyperEngine {
depth = context.getExtendedEventPileup().size();
}
P_of_ref *= 1.0 - (theta / 2.0) * MathUtils.binomialProbability(0, depth, 0.5);
P_of_ref *= 1.0 - (theta / 2.0) * getRefBinomialProb(depth);
}
return new VariantCallContext(vc, QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING, false);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
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@ -26,9 +26,9 @@
package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.genotype.Haplotype;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -29,8 +29,8 @@ import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotype.Haplotype;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

3
public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java → public/java/src/org/broadinstitute/sting/utils/Haplotype.java
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@ -22,10 +22,9 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.genotype;
package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.Allele;

19
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.utils.clipreads;
import com.google.java.contract.Requires;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord;
@ -9,7 +8,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
@ -185,4 +183,21 @@ public class ReadClipper {
}
}
}
public SAMRecord hardClipLeadingInsertions() {
for(CigarElement cigarElement : read.getCigar().getCigarElements()) {
if (cigarElement.getOperator() != CigarOperator.HARD_CLIP && cigarElement.getOperator() != CigarOperator.SOFT_CLIP &&
cigarElement.getOperator() != CigarOperator.INSERTION && cigarElement.getOperator() != CigarOperator.DELETION)
break;
else if (cigarElement.getOperator() == CigarOperator.INSERTION) {
this.addOp(new ClippingOp(0, cigarElement.getLength() - 1));
}
else if (cigarElement.getOperator() == CigarOperator.DELETION) {
throw new ReviewedStingException("No read should start with a deletion. Aligner bug?");
}
}
return clipRead(ClippingRepresentation.HARDCLIP_BASES);
}
}

3
public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
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@ -268,7 +268,8 @@ public class Genotype {
* @param <V> the value type
* @return a sting, enclosed in {}, with comma seperated key value pairs in order of the keys
*/
public static <T extends Comparable<T>, V> String sortedString(Map<T, V> c) {
private static <T extends Comparable<T>, V> String sortedString(Map<T, V> c) {
// NOTE -- THIS IS COPIED FROM GATK UTILS TO ALLOW US TO KEEP A SEPARATION BETWEEN THE GATK AND VCF CODECS
List<T> t = new ArrayList<T>(c.keySet());
Collections.sort(t);

3
public/java/test/org/broadinstitute/sting/utils/genotype/DiploidGenotypeUnitTest.java → public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.utils.genotype;
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;

1
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsUnitTest.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.testng.Assert;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.BaseTest;
import org.testng.annotations.Test;

84
public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java 100644
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@ -0,0 +1,84 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
// our package
package org.broadinstitute.sting.utils.variantcontext;
// the imports for unit testing.
import org.broadinstitute.sting.BaseTest;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.Test;
import java.util.Arrays;
import java.util.List;
public class GenotypeUnitTest extends BaseTest {
Allele A, Aref, T;
@BeforeSuite
public void before() {
A = Allele.create("A");
Aref = Allele.create("A", true);
T = Allele.create("T");
}
// public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased) {
// public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased, double[] log10Likelihoods) {
// public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, double[] log10Likelihoods)
// public Genotype(String sampleName, List<Allele> alleles, double negLog10PError)
// public Genotype(String sampleName, List<Allele> alleles)
// public List<Allele> getAlleles()
// public List<Allele> getAlleles(Allele allele)
// public Allele getAllele(int i)
// public boolean isPhased()
// public int getPloidy()
// public Type getType()
// public boolean isHom()
// public boolean isHomRef()
// public boolean isHomVar()
// public boolean isHet()
// public boolean isNoCall()
// public boolean isCalled()
// public boolean isAvailable()
// public boolean hasLikelihoods()
// public GenotypeLikelihoods getLikelihoods()
// public boolean sameGenotype(Genotype other)
// public boolean sameGenotype(Genotype other, boolean ignorePhase)
// public String getSampleName()
// public boolean hasNegLog10PError()
// public double getNegLog10PError()
// public double getPhredScaledQual()
// public boolean hasAttribute(String key)
// public Object getAttribute(String key)
// public Object getAttribute(String key, Object defaultValue)
// public String getAttributeAsString(String key, String defaultValue)
// public int getAttributeAsInt(String key, int defaultValue)
// public double getAttributeAsDouble(String key, double defaultValue)
// public boolean getAttributeAsBoolean(String key, boolean defaultValue)
}