zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

1. Removing an old version of the Genotype interface which is no longer being used. Needed to do this now so that the naming conflicts would cease. 

2. Adding a preliminary version of the new Genotype/Allele interface (putting it into refdata/ as the VariantContext really only applies to rods) with updates to VariantContext.  This is by no means complete - further updates coming tomorrow.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2533 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-01-07 05:51:10 +00:00
parent a9245a58e2
commit 6c739e30e0
10 changed files with 465 additions and 611 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

312
java/src/org/broadinstitute/sting/gatk/contexts/VariantContext.java
View File

@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.contexts; package org.broadinstitute.sting.gatk.contexts;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.genotype.Genotype; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.gatk.refdata.*;
import java.util.*; import java.util.*;
import org.apache.commons.jexl.*; import org.apache.commons.jexl.*;
@ -11,159 +11,305 @@ import org.apache.commons.jexl.*;
/** /**
* @author ebanks * @author ebanks
* <p/> * <p/>
* Interface VariantContext * Class VariantContext
* <p/> * <p/>
* This class represents a context that unifies one or more variants * This class represents a context that unifies one or more variants
*/ */
public interface VariantContext { public class VariantContext {
private static final String UNIQUIFIED_SUFFIX = ".unique";
private Set<Allele> alleles;
private Set<Genotype> genotypes;
private Allele reference;
private GenomeLoc loc;
private HashMap<Object, Object> attributes;
public VariantContext(VariationRod rod) {
// TODO -- VariationRod should eventually require classes to implement toVariationContext()
// TODO -- (instead of using a temporary adapter class)
loc = rod.getLocation();
reference = new Allele(Allele.AlleleType.REFERENCE, rod.getReference());
// TODO -- populate the alleles and genotypes through an adapter
alleles = new HashSet<Allele>();
genotypes = new HashSet<Genotype>();
attributes = new HashMap<Object, Object>();
}
protected VariantContext(GenomeLoc loc, Allele reference, Set<Allele> alleles, Set<Genotype> genotypes, HashMap<Object, Object> attributes) {
this.loc = loc;
this.reference = reference;
this.alleles = new HashSet<Allele>(alleles);
this.genotypes = new HashSet<Genotype>(genotypes);
this.attributes = new HashMap<Object, Object>(attributes);
}
/**
* @param other another variant context
*
* throws an exception if there is a collision such that the same sample exists in both contexts
* @return a context representing the merge of this context and the other provided context
*/
public VariantContext merge(VariantContext other) {
return merge(other, false);
}
/**
* @param other another variant context
* @param uniquifySamples if true and there is a collision such that the same sample exists in both contexts,
* the samples will be uniquified(based on their sources);
* otherwise, an exception will be thrown
*
* @return a context representing the merge of this context and the other provided context
*/
public VariantContext merge(VariantContext other, boolean uniquifySamples) {
if ( !loc.equals(other.getLocation()) )
throw new IllegalArgumentException("The locations must be identical for two contexts to be merged");
Set<String> samples = getSampleNames();
Set<Genotype> Gs = new HashSet<Genotype>(genotypes);
for ( Genotype g : other.getGenotypes() ) {
if ( samples.contains(g.getSample()) ) {
if ( uniquifySamples )
g.setSample(g.getSample() + UNIQUIFIED_SUFFIX);
else
throw new IllegalStateException("The same sample name exists in both contexts when attempting to merge");
}
Gs.add(g);
}
HashMap<Object, Object> attrs = new HashMap<Object, Object>(attributes);
attrs.putAll(other.getAttributes());
return createNewContext(Gs, attrs);
}
/** /**
* @return the location of this context * @return the location of this context
*/ */
public GenomeLoc getLocation(); public GenomeLoc getLocation() { return loc; }
/** /**
* @return the reference base or bases for this context, as a string * @return the reference allele for this context
*/ */
public String getReference(); public Allele getReference() { return reference; }
/** /**
* @return true if the context is variant (i.e. contains a non-reference allele) * @return true if the context is variant (i.e. contains a non-reference allele)
*/ */
public boolean isVariant(); public boolean isVariant() {
for ( Allele allele : alleles ) {
if ( allele.isVariant() )
return true;
}
return false;
}
/** /**
* @return true if the context is strictly bi-allelic * @return true if the context is strictly bi-allelic
*/ */
public boolean isBiallelic(); public boolean isBiallelic() {
return getAlternateAlleles().size() == 1;
}
/** /**
* @return true if the context represents point mutations only (i.e. no indels or structural variants) * @return true if the context represents point alleles only (i.e. no indels or structural variants)
*/ */
public boolean isPointMutation(); public boolean isPointAllele() {
for ( Allele allele : alleles ) {
if ( allele.isVariant() && !allele.isSNP() )
return false;
}
return true;
}
/** /**
* @param sample the sample name * @return the set of all sample names in this context
*
* @return true if the context contains data for the given sample
*/ */
public boolean hasSample(String sample); public Set<String> getSampleNames() {
Set<String> samples = new TreeSet<String>();
/** for ( Genotype g : genotypes )
* @param sample the sample name samples.add(g.getSample());
* return samples;
* @return true if the context contains data for only a single instance of the given sample }
*/
public boolean hasSingleInstanceOfSample(String sample);
/**
* @return the number of samples in this context.
* If a given sample has more than one instance in this context, each one is counted separately
*/
public int size();
/**
* @return the number of unique samples in this context
*/
public int numSamples();
/**
* @return the set of all unique sample names in this context
*/
public Set<String> getSampleNames();
/** /**
* @return true if the context represents variants with associated genotypes * @return true if the context represents variants with associated genotypes
*/ */
public boolean hasGenotypes(); public boolean hasGenotypes() { return genotypes.size() > 0; }
/** /**
* @return set of all Genotypes associated with this context * @return set of all Genotypes associated with this context
*/ */
public Set<Genotype> getGenotypes(); public Set<Genotype> getGenotypes() { return genotypes; }
/**
* @param sample the sample name
*
* @return set of all Genotypes associated with the given sample in this context
*/
public Set<Genotype> getGenotypes(String sample);
/** /**
* @param sample the sample name * @param sample the sample name
* *
* @return the Genotype associated with the given sample in this context or null if the sample is not in this context * @return the Genotype associated with the given sample in this context or null if the sample is not in this context
* throws an exception if multiple instances of the sample exist in the context
*/ */
public Genotype getGenotype(String sample); public Genotype getGenotype(String sample) {
for ( Genotype g : genotypes ) {
/** if ( g.getSample().equals(sample) )
* @param sample the sample name return g;
* }
* @return the Variation associated with the given sample in this context or null if the sample is not in this context return null;
*/ }
public Variation toVariation(String sample);
/** /**
* @return set of all subclasses within this context * @return set of all subclasses within this context
*/ */
public Set<String> getSubclasses(); public Set<Object> getSubclasses() {
Set<Object> subclasses = new HashSet<Object>();
for ( Genotype g : genotypes )
subclasses.addAll(g.getAttributes().keySet());
return subclasses;
}
/** /**
* @param subclass the name of a subclass of variants to select * @param subclass the name of a subclass of variants to select
* *
* @return a subset of this context which selects based on the given subclass * @return a subset of this context which selects based on the given subclass
*/ */
public VariantContext select(String subclass); public VariantContext select(String subclass) {
HashSet<Genotype> Gs = new HashSet<Genotype>();
for ( Genotype g : genotypes ) {
if ( g.getAttribute(subclass) != null )
Gs.add(g);
}
return createNewContext(Gs, attributes);
}
/** /**
* @param expr a jexl expression describing how to filter this context * @param expr a jexl expression describing how to filter this context
* *
* @return a subset of this context which is filtered based on the given expression * @return a subset of this context which is filtered based on the given expression
*/ */
public VariantContext filter(String expr); public VariantContext filter(String expr) {
HashSet<Genotype> Gs = new HashSet<Genotype>();
try {
Expression filterExpression = ExpressionFactory.createExpression(expr);
for ( Genotype g : genotypes ) {
JexlContext jContext = JexlHelper.createContext();
jContext.setVars(g.getAttributes());
if ( (Boolean)filterExpression.evaluate(jContext) )
Gs.add(g);
}
} catch (Exception e) {
throw new StingException("JEXL error in VariantContext: " + e.getMessage());
}
return createNewContext(Gs, attributes);
}
/** /**
* @return a set of variant contexts where each one represents (all instances of) a single sample from this context * @return a set of new variant contexts, one for each sample from this context
*/ */
public Set<VariantContext> splitBySample(); public Set<VariantContext> splitBySample() {
Set<VariantContext> contexts = new HashSet<VariantContext>();
for ( Genotype g : genotypes ) {
HashSet<Genotype> gAsSet = new HashSet<Genotype>();
gAsSet.add(g);
contexts.add(createNewContext(gAsSet, attributes));
}
return contexts;
}
/** /**
* get the alternate allele frequency of this variant context, if the context is variable. * @param Gs the set of genotypes from which to create a new context
* If this context is not variable or a frequency cannot be provided, this method should return 0. * @param attrs the attributes for the new context
* *
* WARNING: This method is valid only for bi-allelic contexts; the contract is to check isBiallelic() * @return a new context based on the given genotypes
* before calling this method
*
* @return double the minor allele frequency
*/ */
public double getNonRefAlleleFrequency(); private VariantContext createNewContext(Set<Genotype> Gs, HashMap<Object, Object> attrs) {
HashSet<Allele> As = new HashSet<Allele>();
for ( Genotype g : Gs )
As.addAll(g.getAlleles());
return new VariantContext(loc, reference, As, Gs, attrs);
}
/** /**
* get the -1 * (log 10 of the error value) * @param allele the allele to be queried
* *
* @return the postive number space log based error estimate * @return the frequency of the given allele in this context
*/ */
public double getNegLog10PError(); public double getAlleleFrequency(Allele allele) {
int alleleCount = 0;
int totalCount = 0;
for ( Genotype g : genotypes ) {
for ( Allele a : g.getAlleles() ) {
totalCount++;
if ( allele.equals(a) )
alleleCount++;
}
}
return totalCount == 0 ? 0.0 : (double)alleleCount / (double)totalCount;
}
/** /**
* gets the alleles. This method should return all of the alleles present at the location, * Gets the alleles. This method should return all of the alleles present at the location,
* including the reference base. The first allele should always be the reference allele, followed * including the reference allele. There are no constraints imposed on the ordering of alleles
* by an unordered list of alternate alleles. If the reference base is not an allele in this varation * in the set. If the reference is not an allele in this context it will not be included.
* it will not be in the list (i.e. there is no guarantee that the reference base is in the list).
* *
* @return an alternate allele list * @return the set of alleles
*/ */
public List<String> getAlleles(); public Set<Allele> getAlleles() { return alleles; }
/** /**
* gets the alternate alleles. This method should return all the alleles present at the location, * Gets the alternate alleles. This method should return all the alleles present at the location,
* NOT including the reference base. This is returned as a string list with no guarantee ordering * NOT including the reference allele. There are no constraints imposed on the ordering of alleles
* of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest * in the set.
* frequency).
* *
* @return an alternate allele list * @return the set of alternate alleles
*/ */
public List<String> getAlternateAlleleList(); public Set<Allele> getAlternateAlleles() {
HashSet<Allele> altAlleles = new HashSet<Allele>();
for ( Allele allele : alleles ) {
if ( !allele.equals(reference) )
altAlleles.add(allele);
}
return altAlleles;
}
/**
* Sets the given attribute
*
* @param key the attribute key
* @param value the attribute value
*/
public void setAttribute(Object key, Object value) {
attributes.put(key, value);
}
/**
* @param key the attribute key
*
* @return the attribute value for the given key (or null if not set)
*/
public Object getAttribute(Object key) {
return attributes.get(key);
}
/**
* @return the attribute map
*/
public Map<Object, Object> getAttributes() {
return attributes;
}
} }

79
java/src/org/broadinstitute/sting/gatk/refdata/Allele.java 100755
View File

@ -0,0 +1,79 @@
package org.broadinstitute.sting.gatk.refdata;
/**
* @author ebanks
* <p/>
* Class Allele
* <p/>
* This class emcompasses all the basic information about an allele
*/
public class Allele {
private AlleleType type;
private String bases;
// the types of variants we currently allow
public enum AlleleType {
REFERENCE, SNP, INSERTION, DELETION, INVERSION
}
public Allele(AlleleType type, String bases) {
this.type = type;
if ( bases == null )
throw new IllegalArgumentException("Constructor: the Allele base string cannot be null");
if ( type == AlleleType.DELETION && bases.length() > 0 )
throw new IllegalArgumentException("Constructor: deletions cannot have observed bases");
this.bases = bases.toUpperCase();
}
/**
* convenience method for switching over the allele type
*
* @return the AlleleType of this allele
**/
public AlleleType getType() { return type; }
/**
* convenience method for SNPs
*
* @return true if this is a SNP, false otherwise
*/
public boolean isSNP() { return type == AlleleType.SNP; }
/**
* convenience method for variants
*
* @return true if this is a variant allele, false if it's reference
*/
public boolean isVariant() { return type != AlleleType.REFERENCE; }
/**
* convenience method for indels
*
* @return true if this is an indel, false otherwise
*/
public boolean isIndel() { return type == AlleleType.INSERTION || type == AlleleType.DELETION; }
/**
* For deletions, this method returns an empty String.
* For everything else, observed bases for the allele are returned.
*
* @return the bases, as a string
*/
public String getBases() { return bases; }
/**
* @param other the other allele
*
* @return true if these alleles are equal
*/
public boolean equals(Allele other) {
return type == other.getType() && bases.equals(other.getBases());
}
}

279
java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java 100644 → 100755
View File

@ -1,172 +1,147 @@
package org.broadinstitute.sting.gatk.refdata; package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GenomeLoc; import java.util.*;
import java.util.List;
/** /**
* Created by IntelliJ IDEA. * @author ebanks
* User: asivache * <p/>
* Date: Apr 1, 2009 * Class Genotype
* Time: 11:02:03 AM * <p/>
* To change this template use File | Settings | File Templates. * This class emcompasses all the basic information about a genotype
*/ */
@Deprecated public class Genotype {
public interface Genotype extends Comparable<ReferenceOrderedDatum> {
// ---------------------------------------------------------------------- private List<Allele> alleles;
//
// manipulating the SNP information private double negLog10PError;
//
// ---------------------------------------------------------------------- private String sample;
/** Location of this genotype on the reference (on the forward strand). If the allele is insertion/deletion, the first inserted/deleted base
* is located right <i>after</i> the specified location private HashMap<Object, Object> attributes;
public Genotype(List<Allele> alleles, String sample, double negLog10PError) {
this.alleles = new ArrayList<Allele>(alleles);
this.sample = sample;
this.negLog10PError = negLog10PError;
attributes = new HashMap<Object, Object>();
}
/**
* @return the alleles for this genotype
*/
public List<Allele> getAlleles() { return alleles; }
/**
* @return the ploidy of this genotype
*/
public int getPloidy() { return alleles.size(); }
/**
* @return true if all observed alleles are the same (regardless of whether they are ref or alt)
*/
public boolean isHom() {
// do not assume ploidy == 2
if ( alleles.size() == 0 )
return true;
Allele first = alleles.get(0);
for ( int i = 1; i < alleles.size(); i++ ) {
if ( !first.equals(alleles.get(i)) )
return false;
}
return true;
}
/**
* @return true if we're het (observed alleles differ)
*/
public boolean isHet() { return !isHom(); }
/**
* @return true if this genotype is not actually a genotype but a "no call" (e.g. './.' in VCF)
*/
public boolean isNoCall() {
// TODO -- implement me
return false;
}
/**
* @return true if all alleles for this genotype are SNPs or reference
*/
public boolean isPointGenotype() {
for ( Allele allele : alleles ) {
if ( allele.isVariant() && !allele.isSNP() )
return false;
}
return true;
}
/**
* @return true if this is a variant genotype, false if it's reference
*/
public boolean isVariant() {
for ( Allele allele : alleles ) {
if ( allele.isVariant() )
return true;
}
return false;
}
/**
* @return the -1 * log10-based error estimate
*/
public double getNegLog10PError() { return negLog10PError; }
/**
* @return the sample name
*/
public String getSample() { return sample; }
/**
* Sets the sample name
* *
* @return position on the genome wrapped in GenomeLoc object * @param sample the sample name
*/ */
GenomeLoc getLocation(); public void setSample(String sample) {
this.sample = sample;
}
/** Returns actual observed alleles on the fwd strand. Allowed to return more than two alleles (@see #getPloidy()). /**
* For point genotypes (those that report themselves as isPointGenotype()), the alleles are observed bases. For indels * @param ref the reference base
* (i.e. if isIndelGenotype() is true), a no-event allele is represented by an empty string,
* while the event allele is represented by '+' (insertion) or '-' (deletion) followed by actual inserted or deleted bases.
* @return list of alleles
*/
List<String> getFWDAlleles() ;
/** Returns bases on the fwd strand in the true reference allele (regardless of whether the reference allele
* was observed at this site in this particular genotype!)
* as a String. String can be empty (if alt allele is insertion into
* the reference), can contain a single character (as in SNP or one-base deletion), or multiple characters
* (if alt is a longer deletion). For the actually observed alleles, see #getFWDAlleles()
* *
* @return reference allele, forward strand * @return this genotype as a variation
*/ */
String getFWDRefBases(); // TODO -- implement me
// public Variation toVariation(char ref);
/** Returns reference base (regardless of whether the reference allele was actually observed. This method /**
* is similar to getFWDRefBases() except it returns a single char. For non-point variants (i.e. indels), behavior * Sets the given attribute
* of this method is not specified and can be defined by implementing classes.
* @return
*/
char getRef() ;
/** Returns true if the object represents a point genotype (e.g. reference base vs. a SNP),
* regardless of what the actual observation is (see isReference() and isSNP()).
* @return
*/
boolean isPointGenotype() ;
/** Returns true if the object represents an extended (indel) genotype (e.g. insertion/deletion event vs. no event),
* regardless of what the actual observation is (see isReference(), isIndel(), isInsertion(), isDeletion()).
* @return
*/
boolean isIndelGenotype() ;
/** Is this variant a SNP? Returns true only if this is point genotype AND a non-reference base was observed, false otherwise.
* *
* @return true or false * @param key the attribute key
* @param value the attribute value
*/ */
boolean isSNP(); public void setAttribute(Object key, Object value) {
attributes.put(key, value);
}
/** Returns true if all observed alleles are reference ones (only reference base was observed if this is a point genotype, /**
* or no indel events were observed if this is an indel genotype). All is"Variant" methods (where Variant=SNP,Insertion, etc) should * @param key the attribute key
* return false at a site where isReference() is true to ensure consistency.
* @return
*/
boolean isReference();
/** Is this variant an insertion? Returns true if this is indel genotype AND only insertion event(s) was observed,
* false otherwise. The contract requires isIndel() to return true
* whenever isInsertion() method returns true.
* *
* @return true or false * @return the attribute value for the given key (or null if not set)
*/ */
boolean isInsertion(); public Object getAttribute(Object key) {
return attributes.get(key);
}
/**
/** Is this variant a deletion? Returns true if this is indel genotype AND only deletion event(s) was observed, * @return the attribute map
* false otherwise. The contract requires isIndel() to return true
* whenever isDeletion() method returns true.
*
* @return true or false
*/ */
boolean isDeletion(); public Map<Object, Object> getAttributes() {
return attributes;
}
/** Is this variant an insertion or a deletion? The contract requires
* this to be true if either isInsertion() or isDeletion() returns true. However,
* this method is also allowed to return true even if neither isInsertion()
* nor isDeletion() do (e.g. a het genotype with one insertion and one deletion). Always returns
* false if the object does not represent indel genotype.
* @return
*/
boolean isIndel();
/** Returns phred-scaled confidence for the variation event (e.g. MAQ's SNP confidence, or AlleleCaller's best vs. ref).
*
* @return
*/
double getVariantConfidence();
/** Returns phred-mapped confidence in called genotype (e.g. MAQ's consensus confidence, or AlleleCaller's
* best vs next-best.
* @return
*/
double getConsensusConfidence();
/** Returns true if the site has at most two known or observed alleles (ref and non-ref), or false if there are > 2 allelic variants known or observed. When
* the implementing class is a genotype, alleles should be always counted including the reference allele whether it was observed in the particular
* individual or not: i.e. if the reference is 'C', then both 'CA' and 'AA' genotypes must be reported as bi-allelic, while 'AT' is <i>not</i> bi-allelic (since there are
* two allelic variants, 'A' and 'T' <i>in addition</i> to the (known) reference variant 'C').
* @return
*/
boolean isBiallelic() ;
/** Returns true if both observed alleles are the same (regardless of whether they are ref or alt)
*
* @return
*/
boolean isHom() ;
/** Returns true if observed alleles differ (regardless of whether they are ref or alt)
*
* @return
*/
boolean isHet() ;
/** Returns reference (major) allele base for a SNP variant as a character; should throw IllegalStateException
* if variant is not a SNP.
*
* @return reference base on the forward strand
*/
//char getRefSnpFWD() throws IllegalStateException;
/** Returns bases in the alternative allele as a String. String can be empty (as in deletion from
* the reference), can contain a single character (as in SNP or one-base insertion), or multiple characters
* (for longer indels).
*
* @return alternative allele, forward strand
*/
//String getAltBasesFWD();
/** Returns alternative (minor) allele base for a SNP variant as a character; should throw IllegalStateException
* if variant is not a SNP.
*
* @return alternative allele base on the forward starnd
*/
// char getAltSnpFWD() throws IllegalStateException;
int length();
/** Return actual number of observed alleles (chromosomes) in the genotype.
* @return
*/
// int getPloidy() throws IllegalStateException;
} }

46
java/src/org/broadinstitute/sting/gatk/refdata/GenotypeList.java
View File

@ -1,46 +0,0 @@
package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GenomeLoc;
/** A simple wrapper interface that allows for keeping any of the "main" (point mutation) or "associated" (indel)
* genotypes, or both, at any given reference position. This is the abstraction of "complete" genotyping information:
* one might have or might have not genotyped independently a base at the given position (point) or an indel right after
* that position. The query and getter methods allow clients to figure out what pieces of the genotyping information
* are actually available and to retrieve them. Behavior of the getters when corresponding queries return false is
* not bound by a contract but it is suggested that they return null or a "trivial" (reference) genotype.
*
* @author asivache
*
*/
public interface GenotypeList {
/** Returns true if point mutation genotyping information is available at the
* current position.
* @return
*/
boolean hasPointGenotype();
/** Returns true if indel genotyping information is available at the
* current position.
* @return
*/
boolean hasIndelGenotype();
/** Returns point mutation genotyping information if available;
* behavior is not specified in the case when there is no such information.
* @return
*/
Genotype getPointGenotype();
/** Returns indel genotyping information if available;
* behavior is not specified in the case when there is no such information.
* @return
*/
Genotype getIndelGenotype();
/** Returns position on the reference the stored genotyping data are associated with.
*
* @return
*/
GenomeLoc getLocation();
}

23
java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
View File

@ -29,7 +29,7 @@ import net.sf.samtools.util.StringUtil;
*/ */
public class SAMPileupRecord implements Genotype, GenotypeList { public class SAMPileupRecord {
private static final int NO_VARIANT = -1; private static final int NO_VARIANT = -1;
private static final int SNP_VARIANT = 0; private static final int SNP_VARIANT = 0;
private static final int INSERTION_VARIANT = 1; private static final int INSERTION_VARIANT = 1;
@ -428,13 +428,11 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
* *
* @return reference allele, forward strand * @return reference allele, forward strand
*/ */
@Override
public String getFWDRefBases() { public String getFWDRefBases() {
return refBases; return refBases;
} }
@Override
public List<String> getFWDAlleles() { public List<String> getFWDAlleles() {
return observedAlleles; return observedAlleles;
} }
@ -500,34 +498,28 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
} }
@Override
public double getVariantConfidence() { public double getVariantConfidence() {
return variantScore; return variantScore;
} }
@Override
public boolean isBiallelic() { public boolean isBiallelic() {
return nNonref < 2; return nNonref < 2;
} }
@Override
public double getConsensusConfidence() { public double getConsensusConfidence() {
return consensusScore; return consensusScore;
} }
@Override
public int length() { public int length() {
return eventLength; return eventLength;
} }
@Override
public boolean isIndelGenotype() { public boolean isIndelGenotype() {
return refBaseChar == '*'; return refBaseChar == '*';
} }
@Override
public boolean isPointGenotype() { public boolean isPointGenotype() {
return ! isIndelGenotype(); return ! isIndelGenotype();
} }
@ -537,8 +529,7 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
* point genotype, this method returns null. * point genotype, this method returns null.
* @return * @return
*/ */
@Override public SAMPileupRecord getIndelGenotype() {
public Genotype getIndelGenotype() {
if ( isIndelGenotype() ) return this; if ( isIndelGenotype() ) return this;
else return null; else return null;
} }
@ -548,8 +539,7 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
* indel genotype, this method returns null. * indel genotype, this method returns null.
* @return * @return
*/ */
@Override public SAMPileupRecord getPointGenotype() {
public Genotype getPointGenotype() {
if ( isPointGenotype() ) return this; if ( isPointGenotype() ) return this;
else return null; else return null;
} }
@ -558,7 +548,6 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
* indel genotype is what it only has). * indel genotype is what it only has).
* @return * @return
*/ */
@Override
public boolean hasIndelGenotype() { public boolean hasIndelGenotype() {
return isIndelGenotype(); return isIndelGenotype();
} }
@ -567,13 +556,10 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
* point genotype is what it only has. * point genotype is what it only has.
* @return * @return
*/ */
@Override
public boolean hasPointGenotype() { public boolean hasPointGenotype() {
return isPointGenotype(); return isPointGenotype();
} }
@Override
public int compareTo(ReferenceOrderedDatum o) { public int compareTo(ReferenceOrderedDatum o) {
return getLocation().compareTo(o.getLocation()); return getLocation().compareTo(o.getLocation());
} }
@ -596,7 +582,6 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
rodName = name; rodName = name;
} }
@Override
public boolean hasNext() { public boolean hasNext() {
return parser.hasNext(); return parser.hasNext();
} }
@ -605,7 +590,6 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
* @return the next element in the iteration. * @return the next element in the iteration.
* @throws NoSuchElementException - iterator has no more elements. * @throws NoSuchElementException - iterator has no more elements.
*/ */
@Override
public SAMPileupRecord next() { public SAMPileupRecord next() {
if (!this.hasNext()) throw new NoSuchElementException("SAMPileupRecord next called on iterator with no more elements"); if (!this.hasNext()) throw new NoSuchElementException("SAMPileupRecord next called on iterator with no more elements");
// if ( z == 0 ) t = System.currentTimeMillis(); // if ( z == 0 ) t = System.currentTimeMillis();
@ -621,7 +605,6 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
} }
@Override
public void remove() { public void remove() {
throw new UnsupportedOperationException("'remove' operation is not supported for file-backed SAM pileups"); throw new UnsupportedOperationException("'remove' operation is not supported for file-backed SAM pileups");
} }

10
java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
View File

@ -6,7 +6,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;
public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod { public class SimpleIndelROD extends TabularROD implements VariationRod {
private boolean KGENOMES_FORMAT = false, checkedFormat = false; private boolean KGENOMES_FORMAT = false, checkedFormat = false;
@ -24,7 +24,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
* *
* @return the reference base or bases, as a string * @return the reference base or bases, as a string
*/ */
@Override
public String getReference() { public String getReference() {
return String.valueOf(getRef()); return String.valueOf(getRef());
} }
@ -53,13 +52,11 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
* *
* @return VariantFrequency with the stored frequency * @return VariantFrequency with the stored frequency
*/ */
@Override
public double getNonRefAlleleFrequency() { public double getNonRefAlleleFrequency() {
return 0.0; return 0.0;
} }
/** @return the VARIANT_TYPE of the current variant */ /** @return the VARIANT_TYPE of the current variant */
@Override
public VARIANT_TYPE getType() { public VARIANT_TYPE getType() {
return isInsertion() ? VARIANT_TYPE.INSERTION : VARIANT_TYPE.DELETION; return isInsertion() ? VARIANT_TYPE.INSERTION : VARIANT_TYPE.DELETION;
} }
@ -85,7 +82,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
* *
* @return a char, representing the alternate base * @return a char, representing the alternate base
*/ */
@Override
public char getAlternativeBaseForSNP() { public char getAlternativeBaseForSNP() {
return getAltSnpFWD(); return getAltSnpFWD();
} }
@ -95,7 +91,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
* *
* @return a char, representing the alternate base * @return a char, representing the alternate base
*/ */
@Override
public char getReferenceForSNP() { public char getReferenceForSNP() {
return getRefSnpFWD(); return getRefSnpFWD();
} }
@ -110,7 +105,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
* *
* @return the log based error estimate * @return the log based error estimate
*/ */
@Override
public double getNegLog10PError() { public double getNegLog10PError() {
return getVariationConfidence(); return getVariationConfidence();
} }
@ -123,7 +117,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
* *
* @return an alternate allele list * @return an alternate allele list
*/ */
@Override
public List<String> getAlternateAlleleList() { public List<String> getAlternateAlleleList() {
List<String> ret = getAlleleList(); List<String> ret = getAlleleList();
for (String val : ret) { for (String val : ret) {
@ -139,7 +132,6 @@ public class SimpleIndelROD extends TabularROD implements Genotype, VariationRod
* *
* @return an alternate allele list * @return an alternate allele list
*/ */
@Override
public List<String> getAlleleList() { public List<String> getAlleleList() {
return this.getFWDAlleles(); return this.getFWDAlleles();
} }

13
java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java
View File

@ -30,7 +30,7 @@ import net.sf.picard.reference.ReferenceSequenceFileWalker;
public class rodSAMPileup extends BasicReferenceOrderedDatum implements GenotypeList { public class rodSAMPileup extends BasicReferenceOrderedDatum {
// ---------------------------------------------------------------------- // ----------------------------------------------------------------------
// //
// Constructors // Constructors
@ -71,22 +71,18 @@ public class rodSAMPileup extends BasicReferenceOrderedDatum implements Genotype
return b.toString(); return b.toString();
} }
@Override public SAMPileupRecord getIndelGenotype() {
public Genotype getIndelGenotype() {
return indelGenotype; return indelGenotype;
} }
@Override public SAMPileupRecord getPointGenotype() {
public Genotype getPointGenotype() {
return pointGenotype; return pointGenotype;
} }
@Override
public boolean hasIndelGenotype() { public boolean hasIndelGenotype() {
return indelGenotype != null; return indelGenotype != null;
} }
@Override
public boolean hasPointGenotype() { public boolean hasPointGenotype() {
return pointGenotype != null; return pointGenotype != null;
} }
@ -108,7 +104,6 @@ public class rodSAMPileup extends BasicReferenceOrderedDatum implements Genotype
rodName = name; rodName = name;
} }
@Override
public boolean hasNext() { public boolean hasNext() {
return parser.hasNext(); return parser.hasNext();
} }
@ -117,7 +112,6 @@ public class rodSAMPileup extends BasicReferenceOrderedDatum implements Genotype
* @return the next element in the iteration. * @return the next element in the iteration.
* @throws NoSuchElementException - iterator has no more elements. * @throws NoSuchElementException - iterator has no more elements.
*/ */
@Override
public rodSAMPileup next() { public rodSAMPileup next() {
if (!this.hasNext()) throw new NoSuchElementException("rodSAMPileup next called on iterator with no more elements"); if (!this.hasNext()) throw new NoSuchElementException("rodSAMPileup next called on iterator with no more elements");
rodSAMPileup result = new rodSAMPileup(rodName); rodSAMPileup result = new rodSAMPileup(rodName);
@ -170,7 +164,6 @@ public class rodSAMPileup extends BasicReferenceOrderedDatum implements Genotype
} }
@Override
public void remove() { public void remove() {
throw new UnsupportedOperationException("'remove' operation is not supported for file-backed SAM pileups"); throw new UnsupportedOperationException("'remove' operation is not supported for file-backed SAM pileups");
} }

6
java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
View File

@ -24,7 +24,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
public boolean CONTINUE_AFTER_AN_ERROR = false; public boolean CONTINUE_AFTER_AN_ERROR = false;
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
ReadBackedPileup pileup = context.getPileup(); ReadBackedPileup pileup = context.getBasePileup();
SAMPileupRecord truePileup = getTruePileup( tracker ); SAMPileupRecord truePileup = getTruePileup( tracker );
if ( truePileup == null ) { if ( truePileup == null ) {
@ -105,9 +105,9 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
return null; return null;
if( pileup.hasPointGenotype() ) if( pileup.hasPointGenotype() )
return (SAMPileupRecord)pileup.getPointGenotype(); return pileup.getPointGenotype();
else if( pileup.hasIndelGenotype() ) else if( pileup.hasIndelGenotype() )
return (SAMPileupRecord)pileup.getIndelGenotype(); return pileup.getIndelGenotype();
else else
throw new StingException("Unsupported pileup type: " + pileup); throw new StingException("Unsupported pileup type: " + pileup);
} }

216
java/src/org/broadinstitute/sting/utils/GenotypeUtils.java
View File

@ -1,216 +0,0 @@
package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.gatk.refdata.Genotype;
import org.broadinstitute.sting.gatk.refdata.GenotypeList;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.utils.genotype.Variation;
import java.util.Arrays;
import java.util.List;
/** Holds useful utility methods and auxiliary default classes for working with Genotype objects
*
* @author asivache
*
*/
public class GenotypeUtils {
public static enum VariantType {
POINT, INDEL;
// VariantType() {}
}
/** This method accepts rods that implement either Genotype or GenotypeList interface (all others will result in an exception). Variant
* (Genotype object) of the specified type (point mutation or indel) will be extracted from GenotypeList rod if such variant exists, or the rod itself
* will be typecasted and returned back if it implements Genotype and represents the specified variant type. If the last argument is false, then
* null will be returned in all other cases. If the last argument is true and either a) rod is a GenotypeList that lacks a call of the specified type, but call
* of the other type was made, or b) rod is a Genotype and its type is difference from variant_type, then it will be assumed that the implicit ref/ref call
* of the specified type also exists at this genomic position, and new object representing such default call will be returned. If rod argument
* is null, then this method safely (and silently) returns null.
*
* @param rod GenotypeList or Genotype to extract requested call from/upgrade to requested call
* @param variant_type type of the variant to extract (POINT mutations or INDEL)
* @param assume_implicit_ref_calls true if presence of only a call of different type means that ref/ref call of the requested type is implicitly present
* @return Genotyping call of the requested type or null if no explicit or implicit call was made.
*/
public static Genotype extractGenotype(ReferenceOrderedDatum rod, VariantType variant_type, boolean assume_implicit_ref_calls) {
if ( rod == null ) return null;
if ( rod instanceof GenotypeList ) {
GenotypeList rod_gl = (GenotypeList)rod;
switch ( variant_type ) {
case POINT :
if ( rod_gl.hasPointGenotype() ) return rod_gl.getPointGenotype();
else {
if ( assume_implicit_ref_calls && rod_gl.hasIndelGenotype() ) throw new StingException("Default (reference) implicit POINT genotype is not implemented yet");
else return null;
}
case INDEL:
if ( rod_gl.hasIndelGenotype() ) return rod_gl.getIndelGenotype();
else {
if ( assume_implicit_ref_calls && rod_gl.hasPointGenotype() ) return new DefaultIndelGenotype(rod_gl.getLocation());
else return null;
}
default: throw new StingException("Unrecognized variant type: "+variant_type);
}
} else if ( rod instanceof Genotype ) {
Genotype rod_g = (Genotype)rod;
switch ( variant_type ) {
case POINT:
if ( rod_g.isIndelGenotype() ) {
if ( assume_implicit_ref_calls ) throw new StingException("Default (reference) implicit POINT genotype is not implemented yet");
else return null;
} else return rod_g;
case INDEL:
if ( rod_g.isPointGenotype() ) {
if ( assume_implicit_ref_calls ) return new DefaultIndelGenotype(rod_g.getLocation());
else return null;
} else return rod_g;
default: throw new StingException("Unrecognized variant type: "+variant_type);
}
}
else throw new StingException("track "+rod.getName()+" is not a Genotype or GenotypeList");
}
public static boolean isHet(Variation var) {
if ( var instanceof Genotype )
return ((Genotype)var).isHet();
String genotype = Utils.join("",var.getAlleleList());
if ( genotype.length() < 1 )
return false;
char first = genotype.charAt(0);
for (char base : genotype.toCharArray()) {
if (base != first) return true;
}
return false;
}
/** This class represents a "default" indel-type genotype with homozygous reference (i.e. confidently no indel)
* call. All the interface methods are implemented and return consistent values. Use this class when working with
* genotyping data where absence of explicit indel call actually means that no evidence for an indel was observed
* (SAM pileup is one such example).
* @author asivache
*
*/
public static class DefaultIndelGenotype implements Genotype {
private GenomeLoc location;
private static final List<String> alleles = Arrays.asList("","") ;
private int confidence ;
/** Creates default indel genotype (ref/ref = no indel) at the specified position
* with default consensus confidence of 1000 (variant confidence is 0).
* @param l reference position to associate the genotyping call with
*/
public DefaultIndelGenotype(GenomeLoc l) {
this(l,1000);
}
/** Creates ref/ref (i.e. absense of indel) indel genotype at the specified position
* with the specified consensus confidence (variant confidence is 0).
* @param l reference position to associate the genotyping call with
*/
public DefaultIndelGenotype(GenomeLoc l, int confidence) {
location = l;
this.confidence = confidence;
}
@Override
public double getConsensusConfidence() {
return confidence;
}
@Override
public List<String> getFWDAlleles() {
return alleles;
}
@Override
public String getFWDRefBases() {
return alleles.get(0);
}
@Override
public GenomeLoc getLocation() {
return location;
}
@Override
public char getRef() {
return '*';
}
@Override
public double getVariantConfidence() {
return 0.0;
}
@Override
public boolean isBiallelic() {
return false;
}
@Override
public boolean isDeletion() {
return false;
}
@Override
public boolean isHet() {
return false;
}
@Override
public boolean isHom() {
return true;
}
@Override
public boolean isIndel() {
return false;
}
@Override
public boolean isIndelGenotype() {
return true;
}
@Override
public boolean isInsertion() {
return false;
}
@Override
public boolean isPointGenotype() {
return false;
}
@Override
public boolean isReference() {
return true;
}
@Override
public boolean isSNP() {
return false;
}
@Override
public int length() {
return (int)(location.getStop() - location.getStart() + 1);
}
@Override
public int compareTo(ReferenceOrderedDatum o) {
return location.compareTo(o.getLocation());
}
}
}

52
java/test/org/broadinstitute/sting/utils/GenotypeUtilsTest.java
View File

@ -1,52 +0,0 @@
package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.genotype.BasicVariation;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import java.io.File;
import java.io.FileNotFoundException;
/**
*
* @author aaron
*
* Class GenotypeUtilsTest
*
* a test class for the various function in the genotype utils class
*/
public class GenotypeUtilsTest extends BaseTest {
private static IndexedFastaSequenceFile seq;
private static File vcfFile = new File(validationDataLocation + "vcfexample.vcf");
@BeforeClass
public static void beforeTests() {
try {
seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
} catch (FileNotFoundException e) {
throw new StingException("unable to load the sequence dictionary");
}
GenomeLocParser.setupRefContigOrdering(seq);
}
/**
* make sure that the variation is a het
*/
@Test
public void isHetTest() {
GenomeLoc loc = GenomeLocParser.createGenomeLoc(0,1,2);
BasicVariation var = new BasicVariation("AA", "A", 0, loc,0.0);
Assert.assertTrue(!GenotypeUtils.isHet(var));
BasicVariation var2 = new BasicVariation("AG", "A", 0, loc,0.0);
Assert.assertTrue(GenotypeUtils.isHet(var2));
BasicVariation var3 = new BasicVariation("GG", "A", 0, loc,0.0);
Assert.assertTrue(!GenotypeUtils.isHet(var3));
}
}