From a97184fddf41a7decabd23d93f4f8746bdd9217b Mon Sep 17 00:00:00 2001 From: kiran Date: Wed, 26 Jan 2011 19:33:03 +0000 Subject: [PATCH] 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 --- .../evaluators/GenotypeConcordance.java | 13 ++----- .../evaluators/GenotypePhasingEvaluator.java | 38 +++++++++++-------- 2 files changed, 26 insertions(+), 25 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java index 0a8c1aae5..416ec34d9 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java @@ -7,8 +7,7 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.vcf.VCFConstants; import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.refdata.*; -import org.broadinstitute.sting.gatk.walkers.varianteval.*; -import org.broadinstitute.sting.gatk.walkers.varianteval.StandardEval; +import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.NewEvaluationContext; 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.DataPoint; @@ -45,7 +44,7 @@ import java.util.*; */ @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; protected final static Logger logger = Logger.getLogger(GenotypeConcordance.class); @@ -74,9 +73,7 @@ public class GenotypeConcordance extends org.broadinstitute.sting.gatk.walkers.v private static final int MAX_MISSED_VALIDATION_DATA = 100; - private boolean discordantInteresting = false; - - private VariantEvalWalker.EvaluationContext group = null; + private boolean discordantInteresting = false; static class FrequencyStats implements TableType { class Stats { @@ -249,9 +246,7 @@ public class GenotypeConcordance extends org.broadinstitute.sting.gatk.walkers.v private boolean warnedAboutValidationData = false; - public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) { - this.group = group; - + public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, NewEvaluationContext group) { String interesting = null; // sanity check that we at least have either eval or validation data diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypePhasingEvaluator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypePhasingEvaluator.java index 028a9f274..f8f4cf486 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypePhasingEvaluator.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypePhasingEvaluator.java @@ -1,22 +1,26 @@ 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.VariantContext; -import org.broad.tribble.vcf.VCFConstants; -import org.broadinstitute.sting.gatk.contexts.*; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.gatk.refdata.*; -import org.broadinstitute.sting.gatk.walkers.phasing.*; -import org.broadinstitute.sting.gatk.walkers.varianteval.*; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.phasing.AllelePair; +import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker; +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.tags.Analysis; 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.apache.log4j.Logger; 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 @@ -44,7 +48,7 @@ import java.util.*; */ @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); // a mapping from sample to stats @@ -76,7 +80,8 @@ public class GenotypePhasingEvaluator extends org.broadinstitute.sting.gatk.walk return getName() + ": "; } - 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(); if (ref == null) return interesting.toString(); @@ -153,11 +158,11 @@ public class GenotypePhasingEvaluator extends org.broadinstitute.sting.gatk.walk if (compSampIsPhased || evalSampIsPhased) { if (!evalSampIsPhased) { ps.onlyCompPhased++; - interesting.addReason("ONLY_COMP", samp, group, prevLocus, ""); + //interesting.addReason("ONLY_COMP", samp, group, prevLocus, ""); } else if (!compSampIsPhased) { ps.onlyEvalPhased++; - interesting.addReason("ONLY_EVAL", samp, group, prevLocus, ""); + //interesting.addReason("ONLY_EVAL", samp, group, prevLocus, ""); } else { // both comp and eval are phased: AllelePair prevCompAllelePair = new AllelePair(prevCompAndEval.getCompGenotpye()); @@ -172,13 +177,14 @@ public class GenotypePhasingEvaluator extends org.broadinstitute.sting.gatk.walk Double compPQ = getPQ(compSampGt); Double evalPQ = getPQ(evalSampGt); - if (compPQ != null && evalPQ != null && MathUtils.compareDoubles(compPQ, evalPQ) != 0) - interesting.addReason("PQ_CHANGE", samp, group, prevLocus, compPQ + " -> " + evalPQ); + if (compPQ != null && evalPQ != null && MathUtils.compareDoubles(compPQ, evalPQ) != 0) { + //interesting.addReason("PQ_CHANGE", samp, group, prevLocus, compPQ + " -> " + evalPQ); + } } else { ps.phasesDisagree++; 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)); } } }