Removed support for RMD in @Requires and @Allows
Merge as well Conflicts: private/java/src/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
This commit is contained in:
Mark DePristo
parent
79e4a8f6d3
commit
f6563c0f9f
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@ -370,33 +370,6 @@ public class GenomeAnalysisEngine {
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throw new ArgumentException("Walker does not allow a reference but one was provided.");
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}
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/**
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* Verifies that all required reference-ordered data has been supplied, and any reference-ordered data that was not
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* 'allowed' is still present.
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*
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* @param rods Reference-ordered data to load.
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*/
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protected void validateSuppliedReferenceOrderedData(List<ReferenceOrderedDataSource> rods) {
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// Check to make sure that all required metadata is present.
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List<RMD> allRequired = WalkerManager.getRequiredMetaData(walker);
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for (RMD required : allRequired) {
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boolean found = false;
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for (ReferenceOrderedDataSource rod : rods) {
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if (rod.matchesNameAndRecordType(required.name(), required.type()))
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found = true;
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}
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if (!found)
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throw new ArgumentException(String.format("Walker requires reference metadata to be supplied named '%s' of type '%s', but this metadata was not provided. " +
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"Please supply the specified metadata file.", required.name(), required.type().getSimpleName()));
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}
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// Check to see that no forbidden rods are present.
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for (ReferenceOrderedDataSource rod : rods) {
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if (!WalkerManager.isAllowed(walker, rod))
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throw new ArgumentException(String.format("Walker of type %s does not allow access to metadata: %s", walker.getClass(), rod.getName()));
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}
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}
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protected void validateSuppliedIntervals() {
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// Only read walkers support '-L unmapped' intervals. Trap and validate any other instances of -L unmapped.
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if(!(walker instanceof ReadWalker)) {
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@ -936,7 +909,6 @@ public class GenomeAnalysisEngine {
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flashbackData()));
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// validation: check to make sure everything the walker needs is present, and that all sequence dictionaries match.
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validateSuppliedReferenceOrderedData(dataSources);
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validateSourcesAgainstReference(readsDataSource, referenceDataSource.getReference(), dataSources, builder);
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return dataSources;
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@ -177,19 +177,7 @@ public class WalkerManager extends PluginManager<Walker> {
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* @return The list of allowed reference meta data.
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*/
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public static List<RMD> getAllowsMetaData(Class<? extends Walker> walkerClass) {
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Allows allowsDataSource = getWalkerAllowed(walkerClass);
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if (allowsDataSource == null)
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return Collections.<RMD>emptyList();
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return Arrays.asList(allowsDataSource.referenceMetaData());
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}
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/**
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* Get a list of RODs allowed by the walker.
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* @param walker Walker to query.
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* @return The list of allowed reference meta data.
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*/
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public static List<RMD> getAllowsMetaData(Walker walker) {
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return getAllowsMetaData(walker.getClass());
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return Collections.<RMD>emptyList();
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}
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/**
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@ -226,24 +214,7 @@ public class WalkerManager extends PluginManager<Walker> {
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* @return True if the walker forbids this data type. False otherwise.
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*/
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public static boolean isAllowed(Class<? extends Walker> walkerClass, ReferenceOrderedDataSource rod) {
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Allows allowsDataSource = getWalkerAllowed(walkerClass);
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// Allows is less restrictive than requires. If an allows
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// clause is not specified, any kind of data is allowed.
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if( allowsDataSource == null )
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return true;
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// The difference between unspecified RMD and the empty set of metadata can't be detected.
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// Treat an empty 'allows' as 'allow everything'. Maybe we can have a special RMD flag to account for this
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// case in the future.
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if( allowsDataSource.referenceMetaData().length == 0 )
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return true;
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for( RMD allowed: allowsDataSource.referenceMetaData() ) {
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if( rod.matchesNameAndRecordType(allowed.name(),allowed.type()) )
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return true;
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}
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return false;
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return true;
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}
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/**
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@ -283,8 +254,7 @@ public class WalkerManager extends PluginManager<Walker> {
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* @return The list of required reference meta data.
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*/
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public static List<RMD> getRequiredMetaData(Class<? extends Walker> walkerClass) {
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Requires requiresDataSource = getWalkerRequirements(walkerClass);
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return Arrays.asList(requiresDataSource.referenceMetaData());
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return Collections.emptyList();
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}
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/**
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@ -23,5 +23,4 @@ import java.lang.annotation.*;
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@Target(ElementType.TYPE)
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public @interface Allows {
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DataSource[] value();
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RMD[] referenceMetaData() default {};
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}
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@ -49,7 +49,7 @@ import java.util.TreeSet;
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* the name 'allele' so we know which alternate allele to use at each site.
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*/
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@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
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@Requires(value={},referenceMetaData=@RMD(name="alleles", type= VariantContext.class))
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@Requires(value={})
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@Reference(window=@Window(start=-200,stop=200))
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@By(DataSource.READS)
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@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
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@ -46,7 +46,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
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* Walks along all variant ROD loci, and merges consecutive sites if they segregate in all samples in the ROD.
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*/
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@Allows(value = {DataSource.REFERENCE})
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@Requires(value = {DataSource.REFERENCE}, referenceMetaData = @RMD(name = "variant", type = ReferenceOrderedDatum.class))
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@Requires(value = {DataSource.REFERENCE})
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@By(DataSource.REFERENCE_ORDERED_DATA)
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public class MergeMNPsWalker extends RodWalker<Integer, Integer> {
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@ -49,7 +49,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
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* Walks along all variant ROD loci, and merges consecutive sites if some sample has segregating alt alleles in the ROD.
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*/
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@Allows(value = {DataSource.REFERENCE})
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@Requires(value = {DataSource.REFERENCE}, referenceMetaData = @RMD(name = "variant", type = ReferenceOrderedDatum.class))
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@Requires(value = {DataSource.REFERENCE})
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@By(DataSource.REFERENCE_ORDERED_DATA)
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public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, Integer> {
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@ -311,8 +311,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
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VariantContext newvc = VariantContext.modifyGenotypes(vc, genotypeMap);
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vcfWriter.add(newvc);
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}
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vcfWriter.add(newvc);
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}
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return null;
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@ -56,7 +56,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
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* Walks along all variant ROD loci, caching a user-defined window of VariantContext sites, and then finishes phasing them when they go out of range (using upstream and downstream reads).
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*/
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@Allows(value = {DataSource.READS, DataSource.REFERENCE})
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@Requires(value = {DataSource.READS, DataSource.REFERENCE}, referenceMetaData = @RMD(name = "variant", type = ReferenceOrderedDatum.class))
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@Requires(value = {DataSource.READS, DataSource.REFERENCE})
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@By(DataSource.READS)
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@ReadFilters({MappingQualityZeroReadFilter.class})
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@ -1,228 +0,0 @@
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/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.variantutils;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* Emits specific fields as dictated by the user from one or more VCF files.
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*/
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public class TestRodBindings extends RodWalker<Integer, Integer> {
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@Output(doc="File to which results should be written",required=true)
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protected PrintStream out;
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@Argument(fullName="fields", shortName="F", doc="Fields to emit from the VCF, allows any VCF field, any info field, and some meta fields like nHets", required=true)
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public ArrayList<String> fieldsToTake = new ArrayList<String>();
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@Argument(fullName="showFiltered", shortName="raw", doc="Include filtered records")
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public boolean showFiltered = false;
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@Argument(fullName="maxRecords", shortName="M", doc="Maximum number of records to emit, if provided", required=false)
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public int MAX_RECORDS = -1;
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int nRecords = 0;
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@Argument(fullName="keepMultiAllelic", shortName="KMA", doc="If provided, we will not require the site to be biallelic", required=false)
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public boolean keepMultiAllelic = false;
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@Argument(fullName="allowMissingData", shortName="AMD", doc="If provided, we will not require every record to contain every field", required=false)
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public boolean ALLOW_MISSING_DATA = false;
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@Input(fullName="variants", shortName="V", doc="The variant file we will convert to a table", required=true)
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public RodBinding<VariantContext> variants;
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@Input(fullName="rodList", shortName="RL", doc="A list of ROD types that we will convert to a table", required=true)
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public List<RodBinding<Feature>> variantsList;
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public void initialize() {
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out.println(Utils.join("\t", fieldsToTake));
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}
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public static abstract class Getter { public abstract String get(VariantContext vc); }
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public static Map<String, Getter> getters = new HashMap<String, Getter>();
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static {
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// #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
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getters.put("CHROM", new Getter() { public String get(VariantContext vc) { return vc.getChr(); } });
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getters.put("POS", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getStart()); } });
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getters.put("REF", new Getter() {
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public String get(VariantContext vc) {
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String x = "";
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if (vc.hasAttribute(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY)) {
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Byte refByte = (Byte)(vc.getAttribute(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY));
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x=x+new String(new byte[]{refByte});
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}
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return x+vc.getReference().getDisplayString();
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}
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});
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getters.put("ALT", new Getter() {
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public String get(VariantContext vc) {
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StringBuilder x = new StringBuilder();
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int n = vc.getAlternateAlleles().size();
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if ( n == 0 ) return ".";
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if (vc.hasAttribute(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY)) {
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Byte refByte = (Byte)(vc.getAttribute(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY));
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x.append(new String(new byte[]{refByte}));
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}
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for ( int i = 0; i < n; i++ ) {
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if ( i != 0 ) x.append(",");
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x.append(vc.getAlternateAllele(i).getDisplayString());
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}
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return x.toString();
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}
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});
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getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } });
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getters.put("TRANSITION", new Getter() { public String get(VariantContext vc) {
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if ( vc.isSNP() && vc.isBiallelic() )
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return VariantContextUtils.isTransition(vc) ? "1" : "0";
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else
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return "-1";
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}});
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getters.put("FILTER", new Getter() { public String get(VariantContext vc) {
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return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); }
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});
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getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } });
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getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } });
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getters.put("HOM-VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomVarCount()); } });
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getters.put("NO-CALL", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNoCallCount()); } });
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getters.put("VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount() + vc.getHomVarCount()); } });
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getters.put("NSAMPLES", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNSamples()); } });
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getters.put("NCALLED", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNSamples() - vc.getNoCallCount()); } });
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getters.put("GQ", new Getter() { public String get(VariantContext vc) {
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if ( vc.getNSamples() > 1 ) throw new UserException("Cannot get GQ values for multi-sample VCF");
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return String.format("%.2f", 10 * vc.getGenotype(0).getNegLog10PError());
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}});
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null ) // RodWalkers can make funky map calls
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return 0;
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for ( RodBinding binding : variantsList )
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System.out.printf("VariantList binding %s tags=%s%n", binding, binding.getTags().getPositionalTags());
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if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
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VariantContext vc = tracker.getFirstValue(variants, context.getLocation());
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if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
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List<String> vals = extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA);
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out.println(Utils.join("\t", vals));
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}
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return 1;
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} else {
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if ( nRecords >= MAX_RECORDS ) {
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logger.warn("Calling sys exit to leave after " + nRecords + " records");
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System.exit(0); // todo -- what's the recommend way to abort like this?
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}
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return 0;
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}
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}
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private static final boolean isWildCard(String s) {
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return s.endsWith("*");
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}
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public static List<String> extractFields(VariantContext vc, List<String> fields, boolean allowMissingData) {
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List<String> vals = new ArrayList<String>();
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for ( String field : fields ) {
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String val = "NA";
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if ( getters.containsKey(field) ) {
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val = getters.get(field).get(vc);
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} else if ( vc.hasAttribute(field) ) {
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val = vc.getAttributeAsString(field);
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} else if ( isWildCard(field) ) {
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Set<String> wildVals = new HashSet<String>();
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for ( Map.Entry<String,Object> elt : vc.getAttributes().entrySet()) {
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if ( elt.getKey().startsWith(field.substring(0, field.length() - 1)) ) {
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wildVals.add(elt.getValue().toString());
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}
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}
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if ( wildVals.size() > 0 ) {
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List<String> toVal = new ArrayList<String>(wildVals);
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Collections.sort(toVal);
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val = Utils.join(",", toVal);
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}
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} else if ( ! allowMissingData ) {
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throw new UserException(String.format("Missing field %s in vc %s at %s", field, vc.getSource(), vc));
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}
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if (field.equals("AF") || field.equals("AC")) {
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String afo = val;
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double af=0;
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if (afo.contains(",")) {
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String[] afs = afo.split(",");
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afs[0] = afs[0].substring(1,afs[0].length());
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afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
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double[] afd = new double[afs.length];
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for (int k=0; k < afd.length; k++)
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afd[k] = Double.valueOf(afs[k]);
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af = MathUtils.arrayMax(afd);
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//af = Double.valueOf(afs[0]);
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}
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else
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if (!afo.equals("NA"))
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af = Double.valueOf(afo);
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val = Double.toString(af);
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}
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vals.add(val);
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}
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return vals;
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}
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public Integer reduceInit() {
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return 0;
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}
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public Integer reduce(Integer counter, Integer sum) {
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return counter + sum;
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}
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public void onTraversalDone(Integer sum) {}
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}
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@ -48,7 +48,7 @@ import java.util.*;
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*/
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@Reference(window=@Window(start=0,stop=40))
|
||||
@Requires(value={})
|
||||
public class VariantValidationAssessor extends RodWalker<Pair<VariantContext, Byte>,Integer> {
|
||||
public class VariantValidationAssessor extends RodWalker<VariantContext,Integer> {
|
||||
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
|
||||
public RodBinding<VariantContext> variants;
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue