refactoring: a couple of general purpose (hopefully useful?) methods/classes extracted into a standalone utils class
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@802 348d0f76-0448-11de-a6fe-93d51630548a
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asivache
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@ -19,7 +19,9 @@ import org.broadinstitute.sting.gatk.walkers.RMD;
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import org.broadinstitute.sting.playground.utils.GenotypingCallStats;
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import org.broadinstitute.sting.playground.utils.TrioConcordanceRecord;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenotypeUtils;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.GenotypeUtils.VariantType;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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//@Requires(value=DataSource.REFERENCE,referenceMetaData={@RMD(name="mother",type=rodSAMPileup.class),
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@ -34,18 +36,16 @@ public class MendelianInheritanceWalker extends RefWalker<TrioConcordanceRecord
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@Argument(fullName="log_concordant", shortName="LC",doc="If set, all trio-concordant sites will be logged at level INFO") public boolean LOG_CONCORDANT;
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@Argument(fullName="log_discordant", shortName="LD",doc="If set, all trio-discordant sites will be logged at level INFO") public boolean LOG_DISCORDANT;
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@Argument(fullName="default_reference_calls",shortName="DRC",
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doc="If set to INDEL or POINT, any position where the specified genotype is NOT explicitly specified, while the other (point or indel, respectively) is provided, is considered to be a confident 'reference' (no-indel or no-snp) call")
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public String defCalls;
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doc="If set, any position where the specified genotype is NOT explicitly specified, while the other is provided, is considered to be an implicit confident 'reference' (no-indel or no-snp) call")
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public boolean defCalls;
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@Argument(fullName="variant_type",
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shortName="VT",
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doc="Assess concordance for the variants of the specified type, INDEL or POINT. If genotype track(s) provide both types, the requested one will be selected",
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required=true)
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public String VARIANT_TYPE;
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public GenotypeUtils.VariantType VARIANT_TYPE;
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private static Logger logger = Logger.getLogger(MendelianInheritanceWalker.class);
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private final static String star = new String("*");
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private int variant_type = 1; //0 - point, 1 - indel
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private int default_calls = 0; // 0 - none, 1 - indels, 2 - point, 3 - both
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@Override
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public TrioConcordanceRecord map(RefMetaDataTracker rodData, char ref, LocusContext context) {
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@ -56,54 +56,25 @@ public class MendelianInheritanceWalker extends RefWalker<TrioConcordanceRecord
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ReferenceOrderedDatum rodDad = rodData.lookup("father", null);
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ReferenceOrderedDatum rodKid = rodData.lookup("daughter", null);
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Genotype mom = extractGenotype(rodMom,variant_type);
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Genotype dad = extractGenotype(rodDad,variant_type);
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Genotype kid = extractGenotype(rodKid,variant_type);
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Genotype mom = GenotypeUtils.extractGenotype(rodMom,VARIANT_TYPE,defCalls);
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Genotype dad = GenotypeUtils.extractGenotype(rodDad,VARIANT_TYPE,defCalls);
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Genotype kid = GenotypeUtils.extractGenotype(rodKid,VARIANT_TYPE,defCalls);
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return assessGenotypesInTrio(mom, dad, kid);
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}
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@Override
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/*
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* @Override(non-Javadoc)
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* @see org.broadinstitute.sting.gatk.walkers.Walker#initialize()
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public void initialize() {
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super.initialize();
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VARIANT_TYPE = VARIANT_TYPE.toUpperCase();
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if ( VARIANT_TYPE.equals("POINT")) variant_type = 0;
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else if ( VARIANT_TYPE.equals("INDEL")) variant_type = 1;
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else throw new StingException("Unknown value specified for VARIANT_TYPE. Allowed: POINT, INDEL; passed: "+VARIANT_TYPE);
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if ( defCalls == null ) return;
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defCalls = defCalls.toUpperCase();
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if ( defCalls.equals("INDEL")) default_calls = 1;
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else throw new StingException("POINT or BOTH default calls are not implemented yet");
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};
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private Genotype extractGenotype(ReferenceOrderedDatum gl, int variant_type) {
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if ( gl == null ) return null;
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if ( gl instanceof GenotypeList ) {
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if ( variant_type == 0 ) return ((GenotypeList)gl).getPointGenotype();
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else if ( variant_type == 1 ) {
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if ( ((GenotypeList)gl).hasIndelGenotype() ) return ((GenotypeList)gl).getIndelGenotype();
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else {
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if ( ( default_calls == 1|| default_calls == 3 ) && ((GenotypeList)gl).hasPointGenotype() ) return new DefaultIndelGenotype(gl.getLocation());
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}
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}
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} else if ( gl instanceof Genotype ) {
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switch ( variant_type ) {
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case 0:
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if ( ((Genotype)gl).isIndelGenotype() ) return null;
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else return (Genotype)gl;
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case 1:
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if ( ((Genotype)gl).isPointGenotype() ) return null;
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else return (Genotype)gl;
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default: throw new StingException("Unknown variant type specified");
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}
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}
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else throw new StingException("track "+gl.getName()+" is not a Genotype or GenotypeList");
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return null;
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}
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*/
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/** Takes a single genotype object and returns properly filled new assessment object (covered/assessed/ref/variant set to 0/1
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* according to what the genotype says)
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@ -254,100 +225,6 @@ public class MendelianInheritanceWalker extends RefWalker<TrioConcordanceRecord
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}
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private static class DefaultIndelGenotype implements Genotype {
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private GenomeLoc location;
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private static final List<String> alleles = Arrays.asList("","") ;
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DefaultIndelGenotype(GenomeLoc l) {
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location = l;
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}
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@Override
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public double getConsensusConfidence() {
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return 1000;
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}
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@Override
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public List<String> getFWDAlleles() {
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return alleles;
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}
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@Override
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public String getFWDRefBases() {
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return alleles.get(0);
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}
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@Override
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public GenomeLoc getLocation() {
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return location;
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}
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@Override
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public char getRef() {
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return '*';
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}
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@Override
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public double getVariantConfidence() {
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return 0.0;
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}
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@Override
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public boolean isBiallelic() {
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return false;
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}
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@Override
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public boolean isDeletion() {
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return false;
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}
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@Override
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public boolean isHet() {
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return false;
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}
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@Override
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public boolean isHom() {
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return true;
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}
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@Override
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public boolean isIndel() {
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return false;
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}
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@Override
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public boolean isIndelGenotype() {
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return true;
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}
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@Override
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public boolean isInsertion() {
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return false;
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}
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@Override
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public boolean isPointGenotype() {
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return false;
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}
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@Override
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public boolean isReference() {
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return true;
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}
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@Override
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public boolean isSNP() {
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return false;
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}
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@Override
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public int compareTo(ReferenceOrderedDatum o) {
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return location.compareTo(o.getLocation());
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}
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}
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/*
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protected String shortLine(Genotype av) {
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@ -0,0 +1,196 @@
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package org.broadinstitute.sting.utils;
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import java.util.Arrays;
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import java.util.List;
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import org.broadinstitute.sting.gatk.refdata.Genotype;
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import org.broadinstitute.sting.gatk.refdata.GenotypeList;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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/** Holds useful utility methods and auxiliary default classes for working with Genotype objects
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*
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* @author asivache
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*
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*/
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public class GenotypeUtils {
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public static enum VariantType {
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POINT, INDEL;
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VariantType() {}
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}
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/** This method accepts rods that implement either Genotype or GenotypeList interface (all others will result in an exception). Variant
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* (Genotype object) of the specified type (point mutation or indel) will be extracted from GenotypeList rod if such variant exists, or the rod itself
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* will be typecasted and returned back if it implements Genotype and represents the specified variant type. If the last argument is false, then
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* 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
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* 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
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* of the specified type also exists at this genomic position, and new object representing such default call will be returned. If rod argument
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* is null, then this method safely (and silently) returns null.
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*
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* @param rod GenotypeList or Genotype to extract requested call from/upgrade to requested call
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* @param variant_type type of the variant to extract (POINT mutations or INDEL)
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* @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
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* @return Genotyping call of the requested type or null if no explicit or implicit call was made.
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*/
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public static Genotype extractGenotype(ReferenceOrderedDatum rod, VariantType variant_type, boolean assume_implicit_ref_calls) {
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if ( rod == null ) return null;
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if ( rod instanceof GenotypeList ) {
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GenotypeList rod_gl = (GenotypeList)rod;
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switch ( variant_type ) {
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case POINT :
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if ( rod_gl.hasPointGenotype() ) return rod_gl.getPointGenotype();
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else {
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if ( assume_implicit_ref_calls && rod_gl.hasIndelGenotype() ) throw new StingException("Default (reference) implicit POINT genotype is not implemented yet");
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else return null;
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}
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case INDEL:
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if ( rod_gl.hasIndelGenotype() ) return rod_gl.getIndelGenotype();
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else {
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if ( assume_implicit_ref_calls && rod_gl.hasPointGenotype() ) return new DefaultIndelGenotype(rod_gl.getLocation());
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else return null;
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}
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default: throw new StingException("Unrecognized variant type: "+variant_type);
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}
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} else if ( rod instanceof Genotype ) {
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Genotype rod_g = (Genotype)rod;
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switch ( variant_type ) {
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case POINT:
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if ( rod_g.isIndelGenotype() ) {
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if ( assume_implicit_ref_calls ) throw new StingException("Default (reference) implicit POINT genotype is not implemented yet");
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else return null;
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} else return rod_g;
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case INDEL:
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if ( rod_g.isPointGenotype() ) {
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if ( assume_implicit_ref_calls ) return new DefaultIndelGenotype(rod_g.getLocation());
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else return null;
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} else return rod_g;
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default: throw new StingException("Unrecognized variant type: "+variant_type);
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}
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}
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else throw new StingException("track "+rod.getName()+" is not a Genotype or GenotypeList");
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}
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/** This class represents a "default" indel-type genotype with homozygous reference (i.e. confidently no indel)
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* call. All the interface methods are implemented and return consistent values. Use this class when working with
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* genotyping data where absence of explicit indel call actually means that no evidence for an indel was observed
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* (SAM pileup is one such example).
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* @author asivache
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*
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*/
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public static class DefaultIndelGenotype implements Genotype {
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private GenomeLoc location;
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private static final List<String> alleles = Arrays.asList("","") ;
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private int confidence ;
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/** Creates default indel genotype (ref/ref = no indel) at the specified position
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* with default consensus confidence of 1000 (variant confidence is 0).
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* @param l reference position to associate the genotyping call with
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*/
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public DefaultIndelGenotype(GenomeLoc l) {
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this(l,1000);
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}
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/** Creates ref/ref (i.e. absense of indel) indel genotype at the specified position
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* with the specified consensus confidence (variant confidence is 0).
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* @param l reference position to associate the genotyping call with
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*/
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public DefaultIndelGenotype(GenomeLoc l, int confidence) {
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location = l;
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this.confidence = confidence;
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}
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@Override
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public double getConsensusConfidence() {
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return confidence;
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}
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@Override
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public List<String> getFWDAlleles() {
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return alleles;
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}
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@Override
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public String getFWDRefBases() {
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return alleles.get(0);
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}
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@Override
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public GenomeLoc getLocation() {
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return location;
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}
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@Override
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public char getRef() {
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return '*';
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}
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@Override
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public double getVariantConfidence() {
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return 0.0;
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}
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@Override
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public boolean isBiallelic() {
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return false;
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}
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@Override
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public boolean isDeletion() {
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return false;
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}
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@Override
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public boolean isHet() {
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return false;
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}
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@Override
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public boolean isHom() {
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return true;
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}
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@Override
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public boolean isIndel() {
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return false;
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}
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@Override
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public boolean isIndelGenotype() {
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return true;
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}
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@Override
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public boolean isInsertion() {
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return false;
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}
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@Override
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public boolean isPointGenotype() {
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return false;
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}
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@Override
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public boolean isReference() {
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return true;
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}
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@Override
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public boolean isSNP() {
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return false;
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}
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@Override
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public int compareTo(ReferenceOrderedDatum o) {
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return location.compareTo(o.getLocation());
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}
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}
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}
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