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more cleanup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1631 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-09-15 21:42:03 +00:00
parent 9f7cf73411
commit 542d817688
6 changed files with 67 additions and 36 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/CallableBasesAnalysis.java
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@ -3,10 +3,9 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.Utils;
import java.util.ArrayList;
import java.util.List;
@ -23,7 +22,6 @@ import java.util.List;
public class CallableBasesAnalysis extends BasicVariantAnalysis implements GenotypeAnalysis {
long all_bases = 0;
long all_calls = 0;
//final static double[] Qthresholds = { 10, 20, 30, 40, 50, 100, 200, 500, 1000 };
final static double[] thresholds = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 50, 100};
long[] discoverable_bases = new long[thresholds.length];
long[] genotypable_bases = new long[thresholds.length];
@ -64,14 +62,14 @@ public class CallableBasesAnalysis extends BasicVariantAnalysis implements Genot
// we actually have a record here
if (!(eval instanceof VariantBackedByGenotype)) { // evaluation record isn't a genotype, die!
throw new RuntimeException("Evaluation track isn't an Genotype!");
throw new RuntimeException("Evaluation track isn't backed by a Genotype!");
}
all_calls++;
// For every threshold, updated discoverable and callable
for (int i = 0; i < thresholds.length; i++) {
double threshold = thresholds[i];
DiploidGenotype g = DiploidGenotype.valueOf(Utils.dupString(ref, 2));
DiploidGenotype g = DiploidGenotype.createHomGenotype(ref);
Genotype genotype = ((VariantBackedByGenotype) eval).getGenotype(g);
// update discoverable
if (eval.isSNP() && eval.getNegLog10PError() >= threshold)

5
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -2,9 +2,8 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
import org.broadinstitute.sting.utils.genotype.Variation;
@ -50,7 +49,7 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
if ((chip != null && !(chip instanceof VariantBackedByGenotype) || (eval != null && !(eval instanceof VariantBackedByGenotype))))
throw new StingException("Failure: trying to analyze genotypes of non-genotype data");
DiploidGenotype g = DiploidGenotype.valueOf(Utils.dupString(ref, 2));
DiploidGenotype g = DiploidGenotype.createHomGenotype(ref);
int truthIndex, callIndex;
if (chip == null)
truthIndex = UNKNOWN;

46
java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java
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@ -4,26 +4,38 @@ import org.broadinstitute.sting.utils.GenomeLoc;
/**
*
* @author aaron
*
* Class BasicGenotype
*
* represents a basic genotype object
* @author aaron
* <p/>
* Class BasicGenotype
* <p/>
* represents a basic genotype object. That means that is
* an implementation for a basic genotype call, given the genotype
* string, the ref base, the confidence score, and the location. This
* class currently only represents point genotypes, not indels
*/
public class BasicGenotype implements Genotype {
// the genotype string
private String mGenotype;
// our location
private GenomeLoc mLocation;
// the reference base.
private char mRef;
private double mNetLog10PError;
// the confidence score
private double mNegLog10PError;
/**
* create a basic genotype
* @param genotype
* create a basic genotype, given the following fields
*
* @param location the genomic location
* @param genotype the genotype, as a string, where ploidy = string.length
* @param ref the reference base as a char
* @param negLog10PError the confidence score
*/
public BasicGenotype(GenomeLoc location, String genotype, char ref, double netLog10PError) {
mNetLog10PError = netLog10PError;
public BasicGenotype(GenomeLoc location, String genotype, char ref, double negLog10PError) {
mNegLog10PError = negLog10PError;
mGenotype = genotype;
mLocation = location;
mRef = ref;
@ -32,15 +44,15 @@ public class BasicGenotype implements Genotype {
/**
* get the -1 * (log 10 of the error value)
*
* @return the log based error estimate
* @return the negitive log based error estimate
*/
@Override
public double getNegLog10PError() {
return mNetLog10PError;
return mNegLog10PError;
}
/**
* get the bases that represent this
* get the bases that represent this genotype
*
* @return the bases, as a string
*/
@ -60,7 +72,7 @@ public class BasicGenotype implements Genotype {
}
/**
* Returns true if both observed alleles are the same (regardless of whether they are ref or alt)
* Returns true if both observed allele bases are the same (regardless of whether they are ref or alt)
*
* @return true if we're homozygous, false otherwise
*/
@ -79,7 +91,7 @@ public class BasicGenotype implements Genotype {
}
/**
* Returns true if observed alleles differ (regardless of whether they are ref or alt)
* Returns true if observed allele bases differ (regardless of whether they are ref or alt)
*
* @return true if we're het, false otherwise
*/
@ -138,6 +150,6 @@ public class BasicGenotype implements Genotype {
@Override
public Variation toVariation() {
if (!isVariant(this.mRef)) throw new IllegalStateException("this genotype is not a variant");
return new BasicVariation(this.getBases(),String.valueOf(mRef),this.getBases().length(),mLocation,mNetLog10PError);
return new BasicVariation(this.getBases(), String.valueOf(mRef), this.getBases().length(), mLocation, mNegLog10PError);
}
}

34
java/src/org/broadinstitute/sting/utils/genotype/BasicVariation.java
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@ -3,23 +3,31 @@ package org.broadinstitute.sting.utils.genotype;
import org.broadinstitute.sting.utils.GenomeLoc;
/**
* Created by IntelliJ IDEA.
* User: aaronmckenna
* User: aaron
* Date: Sep 9, 2009
* Time: 9:32:34 PM
* <p/>
* a basic implementation of variant
* a basic implementation of the Variation interface.
*/
public class BasicVariation implements Variation {
// the bases that make up this variant
protected final String mBases;
// the reference base
protected final String mRef;
// the length of the event, 0 for a SNP, negitive for deletions, positive for insertions
protected final int mLength;
// the location on the genome of the event
protected final GenomeLoc mLocation;
// our confidence in this event, and a -(log10(Error))
protected final double mConfidence;
/**
* the constructor
* create a basic variation, given the following parameters:
*
* @param bases the bases that this variant represents
* @param reference the reference bases
@ -34,11 +42,21 @@ public class BasicVariation implements Variation {
mConfidence = confidence;
}
/**
* we don't know the minor allele freq. is this implementation
*
* @return -1.0. If the freq is less than zero it means we don't know
*/
@Override
public double getNonRefAlleleFrequency() {
return -1.0;
}
/**
* get the type of variation we are
*
* @return VARIANT_TYPE
*/
@Override
public VARIANT_TYPE getType() {
if (mLength > 0) return VARIANT_TYPE.INDEL;
@ -84,7 +102,7 @@ public class BasicVariation implements Variation {
@Override
public boolean isReference() {
if (mLength != 0) return true;
if (mLength != 0) return false;
int refIndex = 0;
for (char c : mBases.toCharArray()) {
if (mRef.charAt(refIndex) != c) return false;
@ -93,7 +111,7 @@ public class BasicVariation implements Variation {
}
/**
* are we an insertion or a deletion? yes, then return true. No? Well, false it is.
* are we an insertion or a deletion? yes, then return true.
*
* @return true if we're an insertion or deletion
*/
@ -111,6 +129,8 @@ public class BasicVariation implements Variation {
@Override
public char getAlternativeBaseForSNP() {
if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
// we know that if we're a snp, the reference is a single base, so charAt(0) is safe
if (getAlternateBases().charAt(0) == this.getReference().charAt(0))
return getAlternateBases().charAt(1);
return getAlternateBases().charAt(0);
@ -124,6 +144,8 @@ public class BasicVariation implements Variation {
@Override
public char getReferenceForSNP() {
if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
// we know that if we're a snp, the reference is a single base, so charAt(0) is safe
if (getAlternateBases().charAt(0) == this.getReference().charAt(0))
return getAlternateBases().charAt(0);
return getAlternateBases().charAt(1);

2
java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
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@ -58,7 +58,7 @@ public enum DiploidGenotype {
* @param hom the character to turn into a hom genotype, i.e. if it is A, then returned will be AA
* @return the diploid genotype
*/
public static DiploidGenotype createGenotype(char hom) {
public static DiploidGenotype createHomGenotype(char hom) {
return DiploidGenotype.valueOf((String.valueOf(hom) + String.valueOf(hom)).toUpperCase());
}
}

8
java/test/org/broadinstitute/sting/utils/genotype/DiploidGenotypeTest.java
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@ -83,19 +83,19 @@ public class DiploidGenotypeTest extends BaseTest {
@Test
public void testCreateGenotype() {
char ref = 'A';
DiploidGenotype g = DiploidGenotype.createGenotype(ref);
DiploidGenotype g = DiploidGenotype.createHomGenotype(ref);
Assert.assertTrue("AA".equals(g.toString()));
ref = 'a';
g = DiploidGenotype.createGenotype(ref);
g = DiploidGenotype.createHomGenotype(ref);
Assert.assertTrue("AA".equals(g.toString()));
ref = 't';
g = DiploidGenotype.createGenotype(ref);
g = DiploidGenotype.createHomGenotype(ref);
Assert.assertTrue("TT".equals(g.toString()));
ref = 'T';
g = DiploidGenotype.createGenotype(ref);
g = DiploidGenotype.createHomGenotype(ref);
Assert.assertTrue("TT".equals(g.toString()));
}