Prototype of RODBinding @Arguments instead of -B syntax
Initial version of RodBinding class. Flow from walker Rodbinding @Arguments -> RMDTriplet (old system) -> GATK engine (standard). Will need refactoring.
This commit is contained in:
Mark DePristo
parent
2a51543693
commit
38969b9783
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import java.io.File;
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import java.lang.annotation.Annotation;
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import java.lang.reflect.*;
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import java.util.*;
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@ -275,6 +276,35 @@ public abstract class ArgumentTypeDescriptor {
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}
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}
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/**
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* Parser for RodBinding objects
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*/
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class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
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/**
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* We only want RodBinding class objects
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* @param type The type to check.
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* @return true if the provided class is a RodBinding.class
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*/
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@Override
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public boolean supports( Class type ) {
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return isRodBinding(type);
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}
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public static boolean isRodBinding( Class type ) {
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return type.isAssignableFrom(RodBinding.class);
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}
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@Override
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public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches) {
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ArgumentDefinition defaultDefinition = createDefaultArgumentDefinition(source);
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String value = getArgumentValue( defaultDefinition, matches );
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RodBinding<Object> result = new RodBinding<Object>(source.field.getName(), new File(value));
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Tags tags = getArgumentTags(matches);
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parsingEngine.addTags(result,tags);
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return result;
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}
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}
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/**
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* Parse simple argument types: java primitives, wrapper classes, and anything that has
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* a simple String constructor.
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@ -282,9 +312,10 @@ public abstract class ArgumentTypeDescriptor {
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class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
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@Override
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public boolean supports( Class type ) {
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if( type.isPrimitive() ) return true;
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if( type.isEnum() ) return true;
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if( primitiveToWrapperMap.containsValue(type) ) return true;
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if ( RodBindingArgumentTypeDescriptor.isRodBinding(type) ) return false;
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if ( type.isPrimitive() ) return true;
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if ( type.isEnum() ) return true;
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if ( primitiveToWrapperMap.containsValue(type) ) return true;
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try {
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type.getConstructor(String.class);
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@ -385,7 +416,6 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
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public Object parse(ParsingEngine parsingEngine,ArgumentSource source, Class type, ArgumentMatches matches) {
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Class componentType;
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Object result;
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Tags tags;
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if( Collection.class.isAssignableFrom(type) ) {
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@ -64,6 +64,7 @@ public class ParsingEngine {
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* The type of set used must be ordered (but not necessarily sorted).
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*/
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private static final Set<ArgumentTypeDescriptor> STANDARD_ARGUMENT_TYPE_DESCRIPTORS = new LinkedHashSet<ArgumentTypeDescriptor>( Arrays.asList(new SimpleArgumentTypeDescriptor(),
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new RodBindingArgumentTypeDescriptor(),
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new CompoundArgumentTypeDescriptor(),
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new MultiplexArgumentTypeDescriptor()) );
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@ -0,0 +1,63 @@
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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.commandline;
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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.utils.GenomeLoc;
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import java.io.File;
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import java.util.List;
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/**
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*
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*/
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// TODO -- should have a derived class called VariantContentRodBinding with simple accessors
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public class RodBinding<T> {
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final String variableName;
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final File sourceFile;
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public RodBinding(final String variableName, final File sourceFile) {
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this.variableName = variableName;
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this.sourceFile = sourceFile;
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}
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public String getVariableName() {
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return variableName;
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}
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public File getSourceFile() {
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return sourceFile;
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}
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public List<T> getAll(RefMetaDataTracker tracker) {
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return (List<T>)tracker.getReferenceMetaData(variableName);
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}
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public T getVariantContext(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc) {
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return (T)tracker.getVariantContext(ref, variableName, loc);
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}
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}
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@ -25,8 +25,10 @@
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package org.broadinstitute.sting.gatk;
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import org.broadinstitute.sting.commandline.ArgumentSource;
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import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
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import org.broadinstitute.sting.commandline.CommandLineProgram;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
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import org.broadinstitute.sting.gatk.filters.ReadFilter;
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import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
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@ -34,12 +36,15 @@ import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescripto
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import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
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import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
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import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
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import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import org.broadinstitute.sting.utils.classloader.JVMUtils;
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import org.broadinstitute.sting.utils.text.ListFileUtils;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.List;
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/**
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* @author aaron
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@ -81,7 +86,6 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
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// File lists can require a bit of additional expansion. Set these explicitly by the engine.
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engine.setSAMFileIDs(ListFileUtils.unpackBAMFileList(getArgumentCollection().samFiles,parser));
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engine.setReferenceMetaDataFiles(ListFileUtils.unpackRODBindings(getArgumentCollection().RODBindings,getArgumentCollection().DBSNPFile,parser));
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engine.setWalker(walker);
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walker.setToolkit(engine);
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@ -96,6 +100,11 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
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loadArgumentsIntoObject(walker);
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argumentSources.add(walker);
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Collection<RMDTriplet> newStyle = ListFileUtils.unpackRODBindings(getRodBindingsInWalker(walker), parser);
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Collection<RMDTriplet> oldStyle = ListFileUtils.unpackRODBindings(getArgumentCollection().RODBindings, getArgumentCollection().DBSNPFile, parser);
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oldStyle.addAll(newStyle);
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engine.setReferenceMetaDataFiles(oldStyle);
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for (ReadFilter filter: filters) {
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loadArgumentsIntoObject(filter);
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argumentSources.add(filter);
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@ -112,6 +121,20 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
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return 0;
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}
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private List<RodBinding> getRodBindingsInWalker(Walker<?,?> walker) {
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List<RodBinding> rods = new ArrayList<RodBinding>();
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for ( ArgumentSource source : parser.extractArgumentSources(walker.getClass()) ) {
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Object obj = JVMUtils.getFieldValue(source.field, walker);
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if ( obj instanceof RodBinding ) {
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System.out.printf("Found rod binding for field %s of %s%n", obj, source.field);
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rods.add((RodBinding)obj);
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}
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}
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return rods;
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}
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/**
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* Generate the GATK run report for this walker using the current GATKEngine, if -et is enabled.
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* This report will be written to either STDOUT or to the run repository, depending on the options
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@ -0,0 +1,225 @@
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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.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.commandline.RodBinding;
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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.Requires;
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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 VariantsToTableNewRodStyle 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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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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if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
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VariantContext vc = variants.getVariantContext(tracker, ref, 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);
|
||||
//af = Double.valueOf(afs[0]);
|
||||
|
||||
}
|
||||
else
|
||||
if (!afo.equals("NA"))
|
||||
af = Double.valueOf(afo);
|
||||
|
||||
val = Double.toString(af);
|
||||
|
||||
}
|
||||
vals.add(val);
|
||||
}
|
||||
|
||||
return vals;
|
||||
}
|
||||
|
||||
public Integer reduceInit() {
|
||||
return 0;
|
||||
}
|
||||
|
||||
public Integer reduce(Integer counter, Integer sum) {
|
||||
return counter + sum;
|
||||
}
|
||||
|
||||
public void onTraversalDone(Integer sum) {}
|
||||
}
|
||||
|
|
@ -25,6 +25,7 @@
|
|||
package org.broadinstitute.sting.utils.text;
|
||||
|
||||
import org.broadinstitute.sting.commandline.ParsingEngine;
|
||||
import org.broadinstitute.sting.commandline.RodBinding;
|
||||
import org.broadinstitute.sting.commandline.Tags;
|
||||
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
|
||||
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
|
||||
|
|
@ -93,6 +94,7 @@ public class ListFileUtils {
|
|||
* @return a list of expanded, bound RODs.
|
||||
*/
|
||||
public static Collection<RMDTriplet> unpackRODBindings(final List<String> RODBindings, final String dbSNPFile, final ParsingEngine parser) {
|
||||
// todo -- this is a strange home for this code. Move into ROD system
|
||||
Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();
|
||||
|
||||
for (String fileName: RODBindings) {
|
||||
|
|
@ -134,6 +136,43 @@ public class ListFileUtils {
|
|||
return rodBindings;
|
||||
}
|
||||
|
||||
/**
|
||||
* Convert command-line argument representation of ROD bindings to something more easily understandable by the engine.
|
||||
* @param RODBindings a text equivale
|
||||
* @return a list of expanded, bound RODs.
|
||||
*/
|
||||
public static Collection<RMDTriplet> unpackRODBindings(final List<RodBinding> RODBindings, final ParsingEngine parser) {
|
||||
// todo -- this is a strange home for this code. Move into ROD system
|
||||
Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();
|
||||
|
||||
for (RodBinding rodBinding: RODBindings) {
|
||||
String argValue = rodBinding.getSourceFile().getPath();
|
||||
String fileName = expandFileName(argValue);
|
||||
final Tags tags = parser.getTags(rodBinding);
|
||||
|
||||
List<String> positionalTags = tags.getPositionalTags();
|
||||
if(positionalTags.size() != 1)
|
||||
throw new UserException("Invalid syntax for RODBinding (reference-ordered data) input . " +
|
||||
"Please use the following syntax when providing reference-ordered " +
|
||||
"data: -<arg-name>:<type> <filename>.");
|
||||
// Assume that if tags are present, those tags are name and type.
|
||||
// Name is always first, followed by type.
|
||||
String name = rodBinding.getVariableName();
|
||||
String type = positionalTags.get(0);
|
||||
|
||||
RMDTriplet.RMDStorageType storageType = null;
|
||||
if(tags.getValue("storage") != null)
|
||||
storageType = Enum.valueOf(RMDTriplet.RMDStorageType.class,tags.getValue("storage"));
|
||||
else if(fileName.toLowerCase().endsWith("stdin"))
|
||||
storageType = RMDTriplet.RMDStorageType.STREAM;
|
||||
else
|
||||
storageType = RMDTriplet.RMDStorageType.FILE;
|
||||
|
||||
rodBindings.add(new RMDTriplet(name,type,fileName,storageType,tags));
|
||||
}
|
||||
|
||||
return rodBindings;
|
||||
}
|
||||
|
||||
/**
|
||||
* Expand any special characters that appear in the filename. Right now, '-' is expanded to
|
||||
|
|
|
|||
Loading…
Reference in New Issue