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Removing SlowGenotype object from GATK

This commit is contained in:
Mark DePristo 2012-08-16 15:22:10 -04:00
parent a22e7a5358
commit d8071c66ed
5 changed files with 6 additions and 236 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -233,10 +233,6 @@ public class GenomeAnalysisEngine {
if (args.nonDeterministicRandomSeed)
resetRandomGenerator(System.currentTimeMillis());
// TODO -- REMOVE ME WHEN WE STOP BCF testing
if ( args.USE_SLOW_GENOTYPES )
GenotypeBuilder.MAKE_FAST_BY_DEFAULT = false;
// if the use specified an input BQSR recalibration table then enable on the fly recalibration
if (args.BQSR_RECAL_FILE != null)
setBaseRecalibration(args.BQSR_RECAL_FILE, args.quantizationLevels, args.disableIndelQuals, args.PRESERVE_QSCORES_LESS_THAN, args.emitOriginalQuals);

5
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -379,10 +379,5 @@ public class GATKArgumentCollection {
@Hidden
public boolean generateShadowBCF = false;
// TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed
@Argument(fullName="useSlowGenotypes",shortName = "useSlowGenotypes",doc="",required=false)
@Hidden
public boolean USE_SLOW_GENOTYPES = false;
// TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed
}

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java
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@ -172,7 +172,7 @@ public final class FastGenotype extends Genotype {
* @param values
* @return
*/
private final static boolean validADorPLField(final int[] values) {
private static boolean validADorPLField(final int[] values) {
if ( values != null )
for ( int v : values )
if ( v < 0 )

38
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java
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@ -53,8 +53,6 @@ import java.util.*;
*/
@Invariant({"alleles != null"})
public final class GenotypeBuilder {
public static boolean MAKE_FAST_BY_DEFAULT = true;
private String sampleName = null;
private List<Allele> alleles = Collections.emptyList();
@ -67,8 +65,6 @@ public final class GenotypeBuilder {
private String filters = null;
private int initialAttributeMapSize = 5;
private boolean useFast = MAKE_FAST_BY_DEFAULT;
private final static Map<String, Object> NO_ATTRIBUTES =
Collections.unmodifiableMap(new HashMap<String, Object>(0));
@ -78,31 +74,22 @@ public final class GenotypeBuilder {
//
// -----------------------------------------------------------------
public final static Genotype create(final String sampleName, final List<Allele> alleles) {
public static Genotype create(final String sampleName, final List<Allele> alleles) {
return new GenotypeBuilder(sampleName, alleles).make();
}
public final static Genotype create(final String sampleName,
public static Genotype create(final String sampleName,
final List<Allele> alleles,
final Map<String, Object> attributes) {
return new GenotypeBuilder(sampleName, alleles).attributes(attributes).make();
}
protected final static Genotype create(final String sampleName,
protected static Genotype create(final String sampleName,
final List<Allele> alleles,
final double[] gls) {
return new GenotypeBuilder(sampleName, alleles).PL(gls).make();
}
public final static Genotype create(final String sampleName,
final List<Allele> alleles,
final double log10Perror,
final Map<String, Object> attributes) {
return new GenotypeBuilder(sampleName, alleles)
.GQ(log10Perror == SlowGenotype.NO_LOG10_PERROR ? -1 : (int)(log10Perror * -10))
.attributes(attributes).make();
}
/**
* Create a empty builder. Both a sampleName and alleles must be provided
* before trying to make a Genotype from this builder.
@ -182,23 +169,8 @@ public final class GenotypeBuilder {
*/
@Ensures({"result != null"})
public Genotype make() {
if ( useFast ) {
final Map<String, Object> ea = extendedAttributes == null ? NO_ATTRIBUTES : extendedAttributes;
return new FastGenotype(sampleName, alleles, isPhased, GQ, DP, AD, PL, filters, ea);
} else {
final Map<String, Object> attributes = new LinkedHashMap<String, Object>();
if ( extendedAttributes != null ) attributes.putAll(extendedAttributes);
final double log10PError = GQ == -1 ? SlowGenotype.NO_LOG10_PERROR : (GQ == 0 ? 0 : GQ / -10.0);
if ( DP != -1 ) attributes.put(VCFConstants.DEPTH_KEY, DP);
if ( AD != null ) attributes.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, AD);
final double[] log10likelihoods = PL != null ? GenotypeLikelihoods.fromPLs(PL).getAsVector() : null;
return new SlowGenotype(sampleName, alleles, log10PError, filters, attributes, isPhased, log10likelihoods);
}
}
public GenotypeBuilder useFast(boolean useFast) {
this.useFast = useFast;
return this;
final Map<String, Object> ea = extendedAttributes == null ? NO_ATTRIBUTES : extendedAttributes;
return new FastGenotype(sampleName, alleles, isPhased, GQ, DP, AD, PL, filters, ea);
}
/**

193
public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java
View File

@ -1,193 +0,0 @@
/*
* Copyright (c) 2012, 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.
*/
package org.broadinstitute.sting.utils.variantcontext;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.*;
/**
* This class encompasses all the basic information about a genotype. It is immutable.
*
* @author Mark DePristo
*/
@Deprecated
public class SlowGenotype extends Genotype {
protected CommonInfo commonInfo;
public final static double NO_LOG10_PERROR = CommonInfo.NO_LOG10_PERROR;
protected List<Allele> alleles = null;
protected boolean isPhased = false;
protected SlowGenotype(final String sampleName,
final List<Allele> alleles,
final double log10PError,
final String filters,
final Map<String, Object> attributes,
final boolean isPhased,
final double[] log10Likelihoods) {
super(sampleName, filters);
if ( alleles == null || alleles.isEmpty() )
this.alleles = Collections.emptyList();
else
this.alleles = Collections.unmodifiableList(alleles);
commonInfo = new CommonInfo(sampleName, log10PError, Collections.<String>emptySet(), attributes);
if ( log10Likelihoods != null )
commonInfo.putAttribute(VCFConstants.GENOTYPE_PL_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods));
this.isPhased = isPhased;
validate();
}
@Override public List<Allele> getAlleles() {
return alleles;
}
@Override public Allele getAllele(int i) {
if ( getType() == GenotypeType.UNAVAILABLE )
throw new ReviewedStingException("Requesting alleles for an UNAVAILABLE genotype");
return alleles.get(i);
}
@Override public boolean isPhased() { return isPhased; }
//
// Useful methods for getting genotype likelihoods for a genotype object, if present
//
@Override public boolean hasLikelihoods() {
return (commonInfo.hasAttribute(VCFConstants.GENOTYPE_PL_KEY) && !commonInfo.getAttribute(VCFConstants.GENOTYPE_PL_KEY).equals(VCFConstants.MISSING_VALUE_v4)) ||
(commonInfo.hasAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && !commonInfo.getAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4));
}
@Override public GenotypeLikelihoods getLikelihoods() {
GenotypeLikelihoods x = getLikelihoods(VCFConstants.GENOTYPE_PL_KEY, true);
if ( x != null )
return x;
else {
x = getLikelihoods(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, false);
return x;
}
}
private GenotypeLikelihoods getLikelihoods(String key, boolean asPL) {
Object x = commonInfo.getAttribute(key);
if ( x instanceof String ) {
if ( asPL )
return GenotypeLikelihoods.fromPLField((String)x);
else
return GenotypeLikelihoods.fromGLField((String)x);
}
else if ( x instanceof GenotypeLikelihoods ) return (GenotypeLikelihoods)x;
else return null;
}
private final void validate() {
if ( alleles.size() == 0) return;
for ( Allele allele : alleles ) {
if ( allele == null )
throw new IllegalArgumentException("BUG: allele cannot be null in Genotype");
}
}
// ---------------------------------------------------------------------------------------------------------
//
// get routines to access context info fields
//
// ---------------------------------------------------------------------------------------------------------
@Override public boolean hasLog10PError() { return commonInfo.hasLog10PError(); }
@Override public double getLog10PError() { return commonInfo.getLog10PError(); }
@Override
public boolean hasExtendedAttribute(String key) { return commonInfo.hasAttribute(key); }
@Override
public Object getExtendedAttribute(String key) { return commonInfo.getAttribute(key); }
@Override
public Object getExtendedAttribute(String key, Object defaultValue) {
return commonInfo.getAttribute(key, defaultValue);
}
// public String getAttributeAsString(String key, String defaultValue) { return commonInfo.getAttributeAsString(key, defaultValue); }
// public int getAttributeAsInt(String key, int defaultValue) { return commonInfo.getAttributeAsInt(key, defaultValue); }
// public double getAttributeAsDouble(String key, double defaultValue) { return commonInfo.getAttributeAsDouble(key, defaultValue); }
// public boolean getAttributeAsBoolean(String key, boolean defaultValue) { return commonInfo.getAttributeAsBoolean(key, defaultValue); }
@Override
public int[] getPL() {
return hasPL() ? getLikelihoods().getAsPLs() : null;
}
@Override
public boolean hasPL() {
return hasLikelihoods();
}
@Override
public int getDP() {
return commonInfo.getAttributeAsInt(VCFConstants.DEPTH_KEY, -1);
}
@Override
public boolean hasDP() {
return commonInfo.hasAttribute(VCFConstants.DEPTH_KEY);
}
@Override
public int[] getAD() {
if ( hasAD() ) {
return (int[])commonInfo.getAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS);
} else
return null;
}
@Override
public boolean hasAD() {
return commonInfo.hasAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS);
}
@Override
public int getGQ() {
if ( commonInfo.hasLog10PError() )
return (int)Math.round(commonInfo.getPhredScaledQual());
else
return -1;
}
@Override
public boolean hasGQ() {
return hasLog10PError();
}
@Override
public Map<String, Object> getExtendedAttributes() {
final Map<String, Object> ea = new LinkedHashMap<String, Object>(commonInfo.getAttributes());
for ( final String primary : FastGenotype.PRIMARY_KEYS )
ea.remove(primary);
return ea;
}
}