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Enable family-level stratification (if a ped file is provided)

This commit is contained in:
Laura Gauthier 2015-10-22 12:58:24 -04:00
parent 4fbcfc2e36
commit f7eb5d3082
25 changed files with 185 additions and 34 deletions
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11
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -350,6 +350,17 @@ public class VariantEvalIntegrationTest extends WalkerTest {
executeTestParallel("testVEMendelianViolationEvaluator" + vcfFile, spec);
}
@Test
public void testMVEvalFamilyStrat() {
String vcfFile = "/PhaseByTransmission/PhaseByTransmission.IntegrationTest.TP.vcf";
String pedFile = "/PhaseByTransmission/PhaseByTransmission.IntegrationTest.goodFamilies.ped";
WalkerTestSpec spec = new WalkerTestSpec("-R "+b37KGReference+ " -T VariantEval -ped " + privateTestDir + pedFile + " -eval " + privateTestDir + vcfFile + " -noEV -noST -ST Family -EV MendelianViolationEvaluator -o %s",
1,
Arrays.asList("d599d3e6b308ac06b2c2e003cf596328"));
executeTestParallel("testMVEvalFamilyStrat", spec);
}
private static String withSelect(String cmd, String select, String name) {
return String.format("%s -select '%s' -selectName %s", cmd, select, name);

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java
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@ -140,7 +140,7 @@ public class VariantEvalWalkerUnitTest extends BaseTest {
}
@Override
public List<Object> getRelevantStates(final ReferenceContext ref, final RefMetaDataTracker tracker, final VariantContext comp, final String compName, final VariantContext eval, final String evalName, final String sampleName) {
public List<Object> getRelevantStates(final ReferenceContext ref, final RefMetaDataTracker tracker, final VariantContext comp, final String compName, final VariantContext eval, final String evalName, final String sampleName, final String familyName) {
int i = Integer.valueOf(evalName); // a terrible hack, but we can now provide accessible states
List<Object> states = new ArrayList<Object>();
for ( int state : integers )
@ -180,12 +180,12 @@ public class VariantEvalWalkerUnitTest extends BaseTest {
final RefMetaDataTracker tracker = new RefMetaDataTracker();
final ReferenceContext ref = null;
final VariantContext comp = null;
final String compName = null, sampleName = null;
final String compName = null, sampleName = null, familyName = null;
// increment eval counts for each stratification of divisors of i from from 1...maxI
for ( int i = 1; i <= cfg.maxI; i++ ) {
final String evalName = String.valueOf(i); // terrible hack to stratify by divisor
for ( EvaluationContext nec : VEwalker.getEvaluationContexts(tracker, ref, eval, evalName, comp, compName, sampleName) ) {
for ( EvaluationContext nec : VEwalker.getEvaluationContexts(tracker, ref, eval, evalName, comp, compName, sampleName, familyName) ) {
synchronized (nec) {
nec.apply(tracker, ref, null, comp, eval);
}

81
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java
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@ -29,8 +29,10 @@ import com.google.java.contract.Requires;
import htsjdk.samtools.reference.IndexedFastaSequenceFile;
import htsjdk.samtools.util.IntervalTree;
import htsjdk.samtools.SAMSequenceRecord;
import oracle.jrockit.jfr.StringConstantPool;
import org.apache.log4j.Logger;
import htsjdk.tribble.Feature;
import org.broadinstitute.gatk.engine.samples.Trio;
import org.broadinstitute.gatk.engine.walkers.*;
import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.*;
import org.broadinstitute.gatk.utils.commandline.*;
@ -105,7 +107,7 @@ import java.util.*;
* </pre>
* </p>
*
* <h3>Usage example</h3>
* <h3>Usage examples</h3>
* <pre>
* java -jar GenomeAnalysisTK.jar \
* -T VariantEval \
@ -116,6 +118,18 @@ import java.util.*;
* [--comp comp.vcf]
* </pre>
*
* Count Mendelian violations for each family in a callset with multiple families (and provided pedigree)
* <pre>
* Java -jar GenomeAnalysisTK.jar \
* -T VariantEval \
* -R reference.fasta \
* -o output.MVs.byFamily.table \
* --eval multiFamilyCallset.vcf \
* -noEV -noST \
* -ST Family \
* -EV MendelianViolationEvaluator
* </pre>
*
* <h3>Caveat</h3>
*
* <p>Some stratifications and evaluators are incompatible with each other due to their respective memory requirements,
@ -249,14 +263,18 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
private boolean isSubsettingSamples;
private Set<String> sampleNamesForEvaluation = new LinkedHashSet<String>();
private Set<String> familyNamesForEvaluation = new LinkedHashSet<String>();
private Set<String> sampleNamesForStratification = new LinkedHashSet<String>();
private Set<String> familyNamesForStratification = new LinkedHashSet<String>();
// important stratifications
private boolean byFilterIsEnabled = false;
private boolean perSampleIsEnabled = false;
private boolean perFamilyIsEnabled = false;
// Public constants
private static String ALL_SAMPLE_NAME = "all";
final private static String ALL_SAMPLE_NAME = "all";
final private static String ALL_FAMILY_NAME = "all";
// the number of processed bp for this walker
long nProcessedLoci = 0;
@ -303,12 +321,22 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
final Set<String> allSampleNames = SampleUtils.getSamplesFromCommandLineInput(vcfSamples);
sampleNamesForEvaluation.addAll(new TreeSet<String>(SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS)));
isSubsettingSamples = ! sampleNamesForEvaluation.containsAll(allSampleNames);
familyNamesForEvaluation.addAll(getSampleDB().getFamilyIDs());
if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample")) {
//If stratifying by sample name, assign a stratification for each sample we're evaluating (based on commandline args)...
if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample") ) {
sampleNamesForStratification.addAll(sampleNamesForEvaluation);
}
//...and also a stratification for the sum over all samples
sampleNamesForStratification.add(ALL_SAMPLE_NAME);
//If stratifying by sample name, assign a stratification for each family...
if ( Arrays.asList(STRATIFICATIONS_TO_USE).contains("Family") ) {
familyNamesForStratification.addAll(familyNamesForEvaluation);
}
//...and also a stratification for the sum over all families
familyNamesForStratification.add(ALL_FAMILY_NAME);
// Initialize select expressions
for (VariantContextUtils.JexlVCMatchExp jexl : VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS)) {
SortableJexlVCMatchExp sjexl = new SortableJexlVCMatchExp(jexl.name, jexl.exp);
@ -327,8 +355,17 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
byFilterIsEnabled = true;
else if ( vs.getName().equals("Sample") )
perSampleIsEnabled = true;
else if ( vs.getName().equals("Family"))
perFamilyIsEnabled = true;
}
if (perSampleIsEnabled && perFamilyIsEnabled)
throw new UserException.BadArgumentValue("ST", "Variants cannot be stratified by sample and family at the same time");
if (perFamilyIsEnabled && getSampleDB().getTrios().isEmpty())
throw new UserException.BadArgumentValue("ST", "Cannot stratify by family without *.ped file");
if ( intervalsFile != null ) {
boolean fail = true;
for ( final VariantStratifier vs : stratificationObjects ) {
@ -420,17 +457,24 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
// }
// --------- track --------- sample - VariantContexts -
HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, mergeEvals);
HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false, false);
HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, perFamilyIsEnabled, mergeEvals);
HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false, false, false);
// for each eval track
for ( final RodBinding<VariantContext> evalRod : evals ) {
final Map<String, Collection<VariantContext>> emptyEvalMap = Collections.emptyMap();
final Map<String, Collection<VariantContext>> evalSet = evalVCs.containsKey(evalRod) ? evalVCs.get(evalRod) : emptyEvalMap;
Set<String> statificationLevels;
// for each sample stratifier
for ( final String sampleName : sampleNamesForStratification ) {
Collection<VariantContext> evalSetBySample = evalSet.get(sampleName);
if (perFamilyIsEnabled)
statificationLevels = familyNamesForStratification;
else
statificationLevels = sampleNamesForStratification;
for ( final String stratLevelName : statificationLevels ) {
Collection<VariantContext> evalSetBySample = evalSet.get(stratLevelName);
if ( evalSetBySample == null ) {
evalSetBySample = new HashSet<VariantContext>(1);
evalSetBySample.add(null);
@ -452,7 +496,18 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
// find the comp
final VariantContext comp = findMatchingComp(eval, compSet);
for ( EvaluationContext nec : getEvaluationContexts(tracker, ref, eval, evalRod.getName(), comp, compRod.getName(), sampleName) ) {
Collection<EvaluationContext> contextsForStratification;
if (perFamilyIsEnabled)
contextsForStratification = getEvaluationContexts(tracker, ref, eval, evalRod.getName(), comp, compRod.getName(), null, stratLevelName);
else {
String familyID;
if (stratLevelName.equals("all"))
familyID = "all";
else
familyID = getSampleDB().getSample(stratLevelName).getFamilyID();
contextsForStratification = getEvaluationContexts(tracker, ref, eval, evalRod.getName(), comp, compRod.getName(), stratLevelName, familyID);
}
for ( EvaluationContext nec : contextsForStratification ) {
// eval against the comp
synchronized (nec) {
@ -521,10 +576,11 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
final String evalName,
final VariantContext comp,
final String compName,
final String sampleName ) {
final String sampleName,
final String familyName) {
final List<List<Object>> states = new LinkedList<List<Object>>();
for ( final VariantStratifier vs : stratManager.getStratifiers() ) {
states.add(vs.getRelevantStates(ref, tracker, comp, compName, eval, evalName, sampleName));
states.add(vs.getRelevantStates(ref, tracker, comp, compName, eval, evalName, sampleName, familyName));
}
return stratManager.values(states);
}
@ -649,6 +705,7 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
public double getMendelianViolationQualThreshold() { return MENDELIAN_VIOLATION_QUAL_THRESHOLD; }
public static String getAllSampleName() { return ALL_SAMPLE_NAME; }
public static String getAllFamilyName() { return ALL_FAMILY_NAME; }
public List<RodBinding<VariantContext>> getKnowns() { return knowns; }
@ -657,6 +714,8 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
public boolean isSubsettingToSpecificSamples() { return isSubsettingSamples; }
public Set<String> getSampleNamesForEvaluation() { return sampleNamesForEvaluation; }
public Set<String> getFamilyNamesForEvaluation() { return familyNamesForEvaluation; }
public int getNumberOfSamplesForEvaluation() {
if (sampleNamesForEvaluation!= null && !sampleNamesForEvaluation.isEmpty())
return sampleNamesForEvaluation.size();
@ -667,6 +726,8 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
}
public Set<String> getSampleNamesForStratification() { return sampleNamesForStratification; }
public Set<String> getFamilyNamesForStratification() { return familyNamesForStratification; }
public List<RodBinding<VariantContext>> getComps() { return comps; }
public Set<SortableJexlVCMatchExp> getJexlExpressions() { return jexlExpressions; }

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
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@ -172,7 +172,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
HomVarHet_inheritedRef += mv.getParentsVarHetInheritedRef();
HomVarHet_inheritedVar += mv.getParentsVarHetInheritedVar();
if(mv.getFamilyCalledCount()>0){
if(mv.getFamilyCalledCount()>0 || mv.getFamilyLowQualsCount()>0 || mv.getFamilyCalledCount()>0){
nVariants++;
nFamCalled += mv.getFamilyCalledCount();
nLowQual += mv.getFamilyLowQualsCount();

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java
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@ -67,7 +67,7 @@ public class AlleleCount extends VariantStratifier {
getVariantEvalWalker().getLogger().info("AlleleCount using " + nchrom + " chromosomes");
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String familyName) {
if (eval != null) {
int AC = 0; // by default, the site is considered monomorphic

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java
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@ -47,7 +47,7 @@ public class AlleleFrequency extends VariantStratifier {
}
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
if (eval != null) {
try {
return Collections.singletonList((Object)String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF", 0.0) / 5.0, 3))));

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java
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@ -45,7 +45,7 @@ public class CompRod extends VariantStratifier implements RequiredStratification
}
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
return Collections.singletonList((Object)compName);
}
}

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java
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@ -44,7 +44,7 @@ public class Contig extends VariantStratifier {
}
@Override
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
if (eval != null) {
return Arrays.asList((Object)"all", eval.getChr());
} else {

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java
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@ -53,7 +53,7 @@ public class CpG extends VariantStratifier {
}
@Override
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
boolean isCpG = false;
if (ref != null && ref.getBases() != null) {
String fwRefBases = new String(ref.getBases());

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java
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@ -103,7 +103,7 @@ public class Degeneracy extends VariantStratifier {
}
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
ArrayList<Object> relevantStates = new ArrayList<Object>();
relevantStates.add("all");

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java
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@ -46,7 +46,7 @@ public class EvalRod extends VariantStratifier implements RequiredStratification
}
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
return Arrays.asList((Object)evalName);
}
}

55
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java 100644
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@ -0,0 +1,55 @@
/*
* Copyright 2012-2015 Broad Institute, Inc.
*
* 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.gatk.tools.walkers.varianteval.stratifications;
import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator;
import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantSummary;
import htsjdk.variant.variantcontext.VariantContext;
import java.util.*;
/**
* Stratifies the eval RODs by each family in the eval ROD, as described by the pedigree.
*
* This allows the system to analyze each family separately. This is particularly useful for the MendelianViolationEvaluator module.
*/
public class Family extends VariantStratifier {
@Override
public void initialize() {
states.addAll(getVariantEvalWalker().getFamilyNamesForStratification());
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String familyName) {
return Collections.singletonList((Object) familyName);
}
@Override
public Set<Class<? extends VariantEvaluator>> getIncompatibleEvaluators() {
return new HashSet<Class<? extends VariantEvaluator>>(Arrays.asList(VariantSummary.class));
}
}

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java
View File

@ -43,7 +43,7 @@ public class Filter extends VariantStratifier {
states.add("raw");
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
ArrayList<Object> relevantStates = new ArrayList<Object>();
relevantStates.add("raw");

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java
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@ -53,7 +53,7 @@ public class FunctionalClass extends VariantStratifier {
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
ArrayList<Object> relevantStates = new ArrayList<Object>();
relevantStates.add("all");

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java
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@ -48,7 +48,7 @@ public class IndelSize extends VariantStratifier {
}
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
if (eval != null && eval.isIndel() && eval.isBiallelic()) {
try {
int eventLength = 0;

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java
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@ -75,7 +75,7 @@ public class IntervalStratification extends VariantStratifier {
states.addAll(Arrays.asList("all", "overlaps.intervals", "outside.intervals"));
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
if (eval != null) {
final GenomeLoc loc = getVariantEvalWalker().getToolkit().getGenomeLocParser().createGenomeLoc(eval);
IntervalTree<GenomeLoc> intervalTree = intervalTreeByContig.get(loc.getContig());

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java
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@ -54,7 +54,7 @@ public class JexlExpression extends VariantStratifier implements StandardStratif
}
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
ArrayList<Object> relevantStates = new ArrayList<Object>();
relevantStates.add("none");

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java
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@ -48,7 +48,7 @@ public class Novelty extends VariantStratifier implements StandardStratification
knowns = getVariantEvalWalker().getKnowns();
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
if (tracker != null && eval != null) {
final Collection<VariantContext> knownComps = tracker.getValues(knowns, ref.getLocus());
for ( final VariantContext c : knownComps ) {

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java
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@ -47,7 +47,7 @@ public class OneBPIndel extends VariantStratifier {
}
@Override
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
if (eval != null && eval.isIndel()) {
for ( int l : eval.getIndelLengths() )
if ( Math.abs(l) > 1 )

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java
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@ -46,7 +46,7 @@ public class Sample extends VariantStratifier {
states.addAll(getVariantEvalWalker().getSampleNamesForStratification());
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
return Collections.singletonList((Object) sampleName);
}

3
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java
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@ -64,7 +64,8 @@ public class SnpEffPositionModifier extends VariantStratifier {
final String compName,
final VariantContext eval,
final String evalName,
final String sampleName)
final String sampleName,
final String FamilyName)
{
final List<Object> relevantStates = new ArrayList<Object>();
if (eval != null && eval.isVariant() && eval.hasAttribute(InfoFieldKey.EFFECT_KEY.getKeyName())) {

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java
View File

@ -48,7 +48,7 @@ public class TandemRepeat extends VariantStratifier {
}
@Override
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
if ( eval == null || ! eval.isIndel() )
return ALL;
else if ( GATKVariantContextUtils.isTandemRepeat(eval, ref.getForwardBases()) ) {

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java
View File

@ -54,7 +54,7 @@ public abstract class VariantStratifier implements Comparable<VariantStratifier>
public abstract void initialize();
public abstract List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName);
public abstract List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String familyName);
// -------------------------------------------------------------------------------------
//

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java
View File

@ -42,7 +42,7 @@ public class VariantType extends VariantStratifier {
states.add(t.toString());
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
return eval == null ? Collections.emptyList() : Collections.singletonList((Object)eval.getType().toString());
}

25
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.gatk.tools.walkers.varianteval.util;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.engine.samples.Sample;
import org.broadinstitute.gatk.utils.commandline.RodBinding;
import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
@ -255,6 +256,7 @@ public class VariantEvalUtils {
boolean byFilter,
boolean subsetBySample,
boolean trackPerSample,
boolean trackPerFamily,
boolean mergeTracks) {
if (tracker == null)
return null;
@ -270,9 +272,10 @@ public class VariantEvalUtils {
// First, filter the VariantContext to represent only the samples for evaluation
VariantContext vcsub = vc;
if (subsetBySample && vc.hasGenotypes())
if ((subsetBySample) && vc.hasGenotypes())
vcsub = getSubsetOfVariantContext(vc, variantEvalWalker.getSampleNamesForEvaluation());
//always add a mapping for all samples together
if ((byFilter || !vcsub.isFiltered())) {
addMapping(mapping, VariantEval.getAllSampleName(), vcsub);
}
@ -287,6 +290,26 @@ public class VariantEvalUtils {
}
}
}
else if (vc.hasGenotypes() && trackPerFamily) {
for (final String familyName : variantEvalWalker.getFamilyNamesForEvaluation()) {
Set<String> familyMemberNames = new HashSet<>();
//if the current stratification family name is "all", then add all the families to the VC for evaluation here
if (familyName.equals(VariantEval.getAllFamilyName())) {
familyMemberNames = variantEvalWalker.getSampleNamesForEvaluation();
}
else {
Set<Sample> familyMembers = variantEvalWalker.getToolkit().getSampleDB().getFamily(familyName);
for (final Sample s : familyMembers) {
familyMemberNames.add(s.getID());
}
}
VariantContext samplevc = getSubsetOfVariantContext(vc, familyMemberNames);
if (byFilter || !samplevc.isFiltered()) {
addMapping(mapping, familyName, samplevc);
}
}
}
}
if (mergeTracks && bindings.containsKey(firstTrack)) {