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adding an interface so that the current @Requires with ROD annotations work in walkers like VariantEval 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1700 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-09-23 18:24:05 +00:00
parent ebfbe56b43
commit f783cb30e0
8 changed files with 108 additions and 13 deletions
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5
java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
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@ -5,7 +5,6 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.glf.GLFReader;
import org.broadinstitute.sting.utils.genotype.glf.GLFRecord;
import org.broadinstitute.sting.utils.genotype.glf.SinglePointCall;
@ -14,9 +13,9 @@ import org.broadinstitute.sting.utils.genotype.glf.VariableLengthCall;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.ArrayList;
/**
@ -26,7 +25,7 @@ import java.util.ArrayList;
* <p/>
* the rod class for GLF data.
*/
public class RodGLF implements ReferenceOrderedDatum, Variation, Iterator<RodGLF> {
public class RodGLF implements VariationRod, Iterator<RodGLF> {
static int count = 0;
public GLFReader mReader;
private final String mName;

5
java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
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@ -29,16 +29,15 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.genotype.BasicGenotype;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
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.genotype.VariantBackedByGenotype;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
public class RodGeliText extends BasicReferenceOrderedDatum implements Variation, VariantBackedByGenotype, AllelicVariant {
public class RodGeliText extends BasicReferenceOrderedDatum implements VariationRod, VariantBackedByGenotype, AllelicVariant {
public enum Genotype_Strings {
AA, AC, AG, AT, CC, CG, CT, GG, GT, TT
}

2
java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
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@ -18,7 +18,7 @@ import java.util.regex.Pattern;
* Time: 10:47:14 AM
* To change this template use File | Settings | File Templates.
*/
public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements AllelicVariant, Variation, VariantBackedByGenotype {
public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements AllelicVariant, VariationRod, VariantBackedByGenotype {
private String contig, source, feature, strand, frame;
private long start, stop;
private double score;

2
java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
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@ -25,7 +25,7 @@ import java.util.List;
* <p/>
* An implementation of the ROD for VCF.
*/
public class RodVCF extends BasicReferenceOrderedDatum implements Variation, VariantBackedByGenotype, Iterator<RodVCF> {
public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod, VariantBackedByGenotype, Iterator<RodVCF> {
// our VCF related information
private VCFReader mReader;
public VCFRecord mCurrentRecord;

86
java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
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@ -3,9 +3,10 @@ package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.*;
import java.util.Arrays;
import java.util.List;
public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVariant {
public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVariant, VariationRod {
private boolean KGENOMES_FORMAT = false, checkedFormat = false;
@ -18,6 +19,16 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria
return GenomeLocParser.createGenomeLoc(this.get("0"), pos, (isDeletion() ? pos+length() : pos+1));
}
/**
* get the reference base(s) at this position
*
* @return the reference base or bases, as a string
*/
@Override
public String getReference() {
return String.valueOf(getRef());
}
public List<String> getFWDAlleles() {
if ( is1KGFormat() )
return Arrays.asList(this.get("4"));
@ -36,8 +47,46 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria
public boolean isGenotype() { return false; }
public boolean isPointGenotype() { return false; }
public boolean isIndelGenotype() { return true; }
/**
* get the frequency of this variant
*
* @return VariantFrequency with the stored frequency
*/
@Override
public double getNonRefAlleleFrequency() {
return 0.0;
}
/** @return the VARIANT_TYPE of the current variant */
@Override
public VARIANT_TYPE getType() {
return VARIANT_TYPE.INDEL;
}
public boolean isSNP() { return false; }
public boolean isReference() { return false; }
/**
* gets the alternate base. Use this method if we're biallelic
*
* @return
*/
@Override
public String getAlternateBase() {
return "";
}
/**
* gets the alternate bases. Use this method if teh allele count is greater then 2
*
* @return
*/
@Override
public List<String> getAlternateBases() {
return Arrays.asList(new String[]{""});
}
public boolean isInsertion() {
if ( is1KGFormat() )
return this.get("3").equals("I");
@ -49,10 +98,43 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria
return this.get("3").charAt(0) == '-';
}
public boolean isIndel() { return true; }
/**
* gets the alternate base is the case of a SNP. Throws an IllegalStateException if we're not a SNP
* of
*
* @return a char, representing the alternate base
*/
@Override
public char getAlternativeBaseForSNP() {
return getAltSnpFWD();
}
/**
* gets the reference base is the case of a SNP. Throws an IllegalStateException if we're not a SNP
*
* @return a char, representing the alternate base
*/
@Override
public char getReferenceForSNP() {
return getRefSnpFWD();
}
public double getVariantConfidence() { return 0.0; }
public double getVariationConfidence() { return 0.0; }
public double getConsensusConfidence() { return 0.0; }
public boolean isBiallelic() { return true; }
/**
* get the -1 * (log 10 of the error value)
*
* @return the log based error estimate
*/
@Override
public double getNegLog10PError() {
return getVariationConfidence();
}
public boolean isHom() { return false; }
public boolean isHet() { return false; }
public double getHeterozygosity() { return 0.0; }

15
java/src/org/broadinstitute/sting/gatk/refdata/VariationRod.java 100644
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@ -0,0 +1,15 @@
package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.genotype.Variation;
/**
* @author aaron
* <p/>
* Interface VariationRod
* <p/>
* This interface combines two interfaces: Variation and ReferenceOrderedDatum. This
* was required so that the reference ordered data require attribute would have an interface
* that both specified variation and ROD compliance.
*/
public interface VariationRod extends Variation, ReferenceOrderedDatum {
}

2
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
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@ -18,7 +18,7 @@ import java.util.List;
* Time: 10:47:14 AM
* To change this template use File | Settings | File Templates.
*/
public class rodDbSNP extends BasicReferenceOrderedDatum implements Variation, VariantBackedByGenotype, AllelicVariant {
public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod, VariantBackedByGenotype, AllelicVariant {
public GenomeLoc loc; // genome location of SNP
// Reference sequence chromosome or scaffold
// Start and stop positions in chrom

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -26,8 +26,8 @@ import java.util.*;
*
*/
@By(DataSource.REFERENCE)
@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=RodGeliText.class)}) // right now we have no base variant class for rods, this should change
@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=RodGeliText.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=RodGenotypeChipAsGFF.class), @RMD(name="interval",type=IntervalRod.class)})
@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=VariationRod.class)}) // right now we have no base variant class for rods, this should change
@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=VariationRod.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=RodGenotypeChipAsGFF.class), @RMD(name="interval",type=IntervalRod.class)})
public class VariantEvalWalker extends RefWalker<Integer, Integer> {
@Argument(shortName="minConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
public int minConfidenceScore = -1;