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-dbSNP rod should not implement VariantBackedByGenotype since dbsnp records have no genotype data 

-added code to cache the allele list so it didn't need to get recomputed each time it was requested.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2260 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-04 14:56:48 +00:00
parent 855face681
commit 1e8dcc30da
1 changed files with 17 additions and 61 deletions
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78
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
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@ -2,12 +2,7 @@ package org.broadinstitute.sting.gatk.refdata;
import net.sf.samtools.util.SequenceUtil;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.genotype.BasicGenotype;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
@ -22,7 +17,7 @@ import java.util.List;
* Time: 10:47:14 AM
* To change this template use File | Settings | File Templates.
*/
public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod, VariantBackedByGenotype {
public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod {
public GenomeLoc loc; // genome location of SNP
// Reference sequence chromosome or scaffold
// Start and stop positions in chrom
@ -50,6 +45,10 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
public int weight; // The quality of the alignment
// cache the allele list so it doesn't need to get recomputed each time
private List<String> alleleList = null;
// ----------------------------------------------------------------------
//
// Constructors
@ -73,7 +72,6 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
*
* @return the reference base or bases, as a string
*/
@Override
public String getReference() {
return refBases;
}
@ -83,7 +81,6 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
*
* @return the log based error estimate
*/
@Override
public double getNegLog10PError() {
return 4; // -log10(0.0001)
}
@ -111,14 +108,17 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
* @return an alternate allele list
*/
public List<String> getAlleleList() {
List<String> ret; //ref first!!!!!
if (onFwdStrand())
ret = Arrays.asList(observed.split("/"));
else
ret = Arrays.asList(SequenceUtil.reverseComplement(observed).split("/"));
if (ret.size() > 0 && ret.contains(getReference()) && !ret.get(0).equals(this.getReference()))
Collections.swap(ret,ret.indexOf(getReference()),0);
return ret;
if ( alleleList == null ) {
// add ref first
if ( onFwdStrand() )
alleleList = Arrays.asList(observed.split("/"));
else
alleleList = Arrays.asList(SequenceUtil.reverseComplement(observed).split("/"));
if ( alleleList.size() > 0 && alleleList.contains(getReference()) && !alleleList.get(0).equals(this.getReference()) )
Collections.swap(alleleList, alleleList.indexOf(getReference()), 0);
}
return alleleList;
}
public boolean onFwdStrand() {
@ -130,13 +130,11 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
*
* @return VariantFrequency with the stored frequency
*/
@Override
public double getNonRefAlleleFrequency() {
return 0; // dbSNP doesn't know the allele frequency
}
/** @return the VARIANT_TYPE of the current variant */
@Override
public VARIANT_TYPE getType() {
return VARIANT_TYPE.SNP;
}// ----------------------------------------------------------------------
@ -167,7 +165,6 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
*
* @return a char, representing the alternate base
*/
@Override
public char getAlternativeBaseForSNP() {
if (!isSNP()) throw new StingException("We're not a SNP; called in DbSNP rod at position " + this.loc);
if (!isBiallelic()) throw new StingException("We're not biallelic; at position " + this.loc);
@ -182,7 +179,6 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
*
* @return a char, representing the alternate base
*/
@Override
public char getReferenceForSNP() {
if (!isSNP()) throw new StingException("We're not a SNP; called in DbSNP rod at position " + this.loc);
if (refBases.length() != 1) throw new StingException("The reference base in DbSNP must be zero, at position " + this.loc + " was " + refBases);
@ -280,47 +276,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
}
public boolean isBiallelic() {
// TODO Auto-generated method stub
return observed.indexOf('/') == observed.lastIndexOf('/');
}
/**
* get the genotype
*
* @return a map in lexigraphical order of the genotypes
*/
@Override
public org.broadinstitute.sting.utils.genotype.Genotype getCalledGenotype() {
return new BasicGenotype(getLocation(),
BasicGenotype.alleleListToString(getAlleleList()),
Utils.stringToChar(getReference()),
getNegLog10PError());
}
/**
* get the likelihoods
*
* @return an array in lexigraphical order of the likelihoods
*/
@Override
public List<org.broadinstitute.sting.utils.genotype.Genotype> getGenotypes() {
ArrayList<Genotype> list = new ArrayList<Genotype>();
list.add(getCalledGenotype());
return list;
}
/**
* do we have the specified genotype? not all backedByGenotypes
* have all the genotype data.
*
* @param x the genotype
*
* @return true if available, false otherwise
*/
@Override
public boolean hasGenotype(DiploidGenotype x) {
return (!x.toString().equals(BasicGenotype.alleleListToString(getAlleleList()))) ? false : true;
return getAlleleList().size() == 2;
}
public static rodDbSNP getFirstRealSNP(RODRecordList<ReferenceOrderedDatum> dbsnpList) {