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Frick! Changed to refer to the *playground* version of VariantEvaluator. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5087 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-01-26 19:33:03 +00:00
parent 73e2942c62
commit a97184fddf
2 changed files with 26 additions and 25 deletions
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11
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java
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@ -7,8 +7,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFConstants; import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.varianteval.*; import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.NewEvaluationContext;
import org.broadinstitute.sting.gatk.walkers.varianteval.StandardEval;
import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis;
import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint;
@ -45,7 +44,7 @@ import java.util.*;
*/ */
@Analysis(name = "Genotype Concordance", description = "Determine the genotype concordance between the genotypes in difference tracks") @Analysis(name = "Genotype Concordance", description = "Determine the genotype concordance between the genotypes in difference tracks")
public class GenotypeConcordance extends org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluator implements StandardEval { public class GenotypeConcordance extends VariantEvaluator implements StandardEval {
private static final boolean PRINT_INTERESTING_SITES = true; private static final boolean PRINT_INTERESTING_SITES = true;
protected final static Logger logger = Logger.getLogger(GenotypeConcordance.class); protected final static Logger logger = Logger.getLogger(GenotypeConcordance.class);
@ -76,8 +75,6 @@ public class GenotypeConcordance extends org.broadinstitute.sting.gatk.walkers.v
private boolean discordantInteresting = false; private boolean discordantInteresting = false;
private VariantEvalWalker.EvaluationContext group = null;
static class FrequencyStats implements TableType { static class FrequencyStats implements TableType {
class Stats { class Stats {
public Stats(int found, int missed) { nFound = found; nMissed = missed; } public Stats(int found, int missed) { nFound = found; nMissed = missed; }
@ -249,9 +246,7 @@ public class GenotypeConcordance extends org.broadinstitute.sting.gatk.walkers.v
private boolean warnedAboutValidationData = false; private boolean warnedAboutValidationData = false;
public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) { public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, NewEvaluationContext group) {
this.group = group;
String interesting = null; String interesting = null;
// sanity check that we at least have either eval or validation data // sanity check that we at least have either eval or validation data

38
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypePhasingEvaluator.java
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@ -1,22 +1,26 @@
package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators; package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators;
import org.apache.log4j.Logger;
import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.walkers.phasing.AllelePair;
import org.broadinstitute.sting.gatk.walkers.phasing.*; import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.*; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker; import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker;
import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis; import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis;
import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint; import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType; import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.NewEvaluationContext;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.report.utils.TableType;
import java.util.*; import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
/* /*
* Copyright (c) 2010 The Broad Institute * Copyright (c) 2010 The Broad Institute
@ -44,7 +48,7 @@ import java.util.*;
*/ */
@Analysis(name = "Genotype Phasing Evaluation", description = "Evaluates the phasing of genotypes in different tracks") @Analysis(name = "Genotype Phasing Evaluation", description = "Evaluates the phasing of genotypes in different tracks")
public class GenotypePhasingEvaluator extends org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluator { public class GenotypePhasingEvaluator extends VariantEvaluator {
protected final static Logger logger = Logger.getLogger(GenotypePhasingEvaluator.class); protected final static Logger logger = Logger.getLogger(GenotypePhasingEvaluator.class);
// a mapping from sample to stats // a mapping from sample to stats
@ -76,7 +80,8 @@ public class GenotypePhasingEvaluator extends org.broadinstitute.sting.gatk.walk
return getName() + ": <table>"; return getName() + ": <table>";
} }
public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) { public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, NewEvaluationContext group) {
//public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
Reasons interesting = new Reasons(); Reasons interesting = new Reasons();
if (ref == null) if (ref == null)
return interesting.toString(); return interesting.toString();
@ -153,11 +158,11 @@ public class GenotypePhasingEvaluator extends org.broadinstitute.sting.gatk.walk
if (compSampIsPhased || evalSampIsPhased) { if (compSampIsPhased || evalSampIsPhased) {
if (!evalSampIsPhased) { if (!evalSampIsPhased) {
ps.onlyCompPhased++; ps.onlyCompPhased++;
interesting.addReason("ONLY_COMP", samp, group, prevLocus, ""); //interesting.addReason("ONLY_COMP", samp, group, prevLocus, "");
} }
else if (!compSampIsPhased) { else if (!compSampIsPhased) {
ps.onlyEvalPhased++; ps.onlyEvalPhased++;
interesting.addReason("ONLY_EVAL", samp, group, prevLocus, ""); //interesting.addReason("ONLY_EVAL", samp, group, prevLocus, "");
} }
else { // both comp and eval are phased: else { // both comp and eval are phased:
AllelePair prevCompAllelePair = new AllelePair(prevCompAndEval.getCompGenotpye()); AllelePair prevCompAllelePair = new AllelePair(prevCompAndEval.getCompGenotpye());
@ -172,13 +177,14 @@ public class GenotypePhasingEvaluator extends org.broadinstitute.sting.gatk.walk
Double compPQ = getPQ(compSampGt); Double compPQ = getPQ(compSampGt);
Double evalPQ = getPQ(evalSampGt); Double evalPQ = getPQ(evalSampGt);
if (compPQ != null && evalPQ != null && MathUtils.compareDoubles(compPQ, evalPQ) != 0) if (compPQ != null && evalPQ != null && MathUtils.compareDoubles(compPQ, evalPQ) != 0) {
interesting.addReason("PQ_CHANGE", samp, group, prevLocus, compPQ + " -> " + evalPQ); //interesting.addReason("PQ_CHANGE", samp, group, prevLocus, compPQ + " -> " + evalPQ);
}
} }
else { else {
ps.phasesDisagree++; ps.phasesDisagree++;
logger.debug("SWITCHED locus: " + curLocus); logger.debug("SWITCHED locus: " + curLocus);
interesting.addReason("SWITCH", samp, group, prevLocus, toString(prevCompAllelePair, compAllelePair) + " -> " + toString(prevEvalAllelePair, evalAllelePair)); //interesting.addReason("SWITCH", samp, group, prevLocus, toString(prevCompAllelePair, compAllelePair) + " -> " + toString(prevEvalAllelePair, evalAllelePair));
} }
} }
} }