Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax
(-B:name,type file) as well as the old syntax. Also, a bonus feature: BAMs can now be tagged at the command-line, which should allow us to get rid of some of the hackier calls in GenomeAnalysisEngine. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4105 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna
parent
aa8cf25d08
commit
3dc78855fd
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@ -48,6 +48,11 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
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*/
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public final SortedMap<Integer,List<String>> indices = new TreeMap<Integer,List<String>>();
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/**
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* An ordered, freeform collection of tags.
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*/
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public final List<String> tags;
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/**
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* Create a new argument match, defining its properties later. Used to create invalid arguments.
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*/
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@ -63,6 +68,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
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private ArgumentMatch(String label,ArgumentDefinition definition) {
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this.label = label;
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this.definition = definition;
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this.tags = Collections.emptyList();
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}
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/**
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@ -70,13 +76,21 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
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* @param label Label of the argument match. Must not be null.
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* @param definition The associated definition, if one exists. May be null.
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* @param index Position of the argument. Must not be null.
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* @param tags ordered freeform text tags associated with this argument.
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*/
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public ArgumentMatch( String label, ArgumentDefinition definition, int index ) {
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this( label, definition, index, null );
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public ArgumentMatch( String label, ArgumentDefinition definition, int index, List<String> tags ) {
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this( label, definition, index, null, tags );
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}
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private ArgumentMatch( String label, ArgumentDefinition definition, int index, String value ) {
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/**
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* A simple way of indicating that an argument with the given label and definition exists at this index.
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* @param label Label of the argument match. Must not be null.
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* @param definition The associated definition, if one exists. May be null.
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* @param index Position of the argument. Must not be null.
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* @param value Value for the argument at this position.
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* @param tags ordered freeform text tags associated with this argument.
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*/
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private ArgumentMatch( String label, ArgumentDefinition definition, int index, String value, List<String> tags ) {
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this.label = label;
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this.definition = definition;
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@ -84,6 +98,8 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
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if( value != null )
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values.add(value);
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indices.put(index,values );
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this.tags = tags;
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}
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/**
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@ -161,7 +177,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
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if( nextIndex == null || nextToken == null )
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throw new IllegalStateException( "No more ArgumentMatches are available" );
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ArgumentMatch match = new ArgumentMatch( label, definition, nextIndex, nextToken );
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ArgumentMatch match = new ArgumentMatch( label, definition, nextIndex, nextToken, tags );
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prepareNext();
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return match;
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}
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@ -185,7 +185,7 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
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// Clone the list of argument matches to avoid ConcurrentModificationExceptions.
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for( ArgumentMatch argumentMatch: getUniqueMatches() ) {
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if( argumentMatch.definition == match.definition ) {
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if( argumentMatch.definition == match.definition && argumentMatch.tags.equals(match.tags) ) {
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argumentMatch.mergeInto( match );
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for( int index: match.indices.keySet() )
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argumentMatches.put( index, argumentMatch );
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@ -149,8 +149,8 @@ public class ArgumentSource {
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* @param values String representation of all values passed.
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* @return the parsed value of the object.
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*/
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public Object parse( ArgumentMatches values ) {
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return typeDescriptor.parse( this, values );
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public Object parse( ParsingEngine parsingEngine, ArgumentMatches values ) {
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return typeDescriptor.parse( parsingEngine, this, values );
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}
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/**
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@ -42,7 +42,7 @@ import java.util.*;
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* @author mhanna
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* @version 0.1
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*/
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public abstract class ArgumentTypeDescriptor {
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public abstract class ArgumentTypeDescriptor {
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private static Class[] ARGUMENT_ANNOTATIONS = {Input.class, Output.class, Argument.class};
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/**
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@ -116,12 +116,16 @@ public abstract class ArgumentTypeDescriptor {
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/**
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* Parses an argument source to an object.
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* WARNING! Mandatory side effect of parsing! Each parse routine should register the tags it finds with the proper CommandLineProgram.
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* TODO: Fix this, perhaps with an event model indicating that a new argument has been created.
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*
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* @param parsingEngine The engine responsible for parsing.
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* @param source The source used to find the matches.
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* @param matches The matches for the source.
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* @return The parsed object.
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*/
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public Object parse( ArgumentSource source, ArgumentMatches matches ) {
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return parse( source, source.field.getType(), matches );
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public Object parse(ParsingEngine parsingEngine, ArgumentSource source, ArgumentMatches matches) {
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return parse(parsingEngine, source, source.field.getType(), matches);
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}
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/**
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@ -174,7 +178,7 @@ public abstract class ArgumentTypeDescriptor {
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* @param matches The argument matches for the argument source, or the individual argument match for a scalar if this is being called to help parse a collection.
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* @return The individual parsed object matching the argument match with Class type.
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*/
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public abstract Object parse( ArgumentSource source, Class type, ArgumentMatches matches );
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public abstract Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches );
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/**
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* If the argument source only accepts a small set of options, populate the returned list with
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@ -219,6 +223,20 @@ public abstract class ArgumentTypeDescriptor {
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return argumentValues.size() > 0 ? argumentValues.iterator().next() : null;
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}
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/**
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* Gets the tags associated with a given command-line argument.
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* If the argument matches multiple values, an exception will be thrown.
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* @param matches The matches for the given argument.
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* @return The value of the argument if available, or null if not present.
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*/
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protected List<String> getArgumentTags(ArgumentMatches matches) {
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Set<String> tags = new LinkedHashSet<String>();
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for( ArgumentMatch match: matches ) {
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tags.addAll(match.tags);
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}
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return new ArrayList<String>(tags);
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}
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/**
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* Gets the values of an argument with the given full name, from the collection of ArgumentMatches.
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* @param definition Definition of the argument for which to find matches.
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@ -294,16 +312,19 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
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}
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@Override
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public Object parse( ArgumentSource source, Class type, ArgumentMatches matches ) {
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public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches) {
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if (source.isFlag())
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return true;
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String value = getArgumentValue( createDefaultArgumentDefinition(source), matches );
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ArgumentDefinition defaultDefinition = createDefaultArgumentDefinition(source);
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String value = getArgumentValue( defaultDefinition, matches );
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Object result;
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List<String> tags = getArgumentTags( matches );
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// lets go through the types we support
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try {
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if (type.isPrimitive()) {
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Method valueOf = primitiveToWrapperMap.get(type).getMethod("valueOf",String.class);
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return valueOf.invoke(null,value.trim());
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result = valueOf.invoke(null,value.trim());
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} else if (type.isEnum()) {
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Object[] vals = type.getEnumConstants();
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Object defaultEnumeration = null; // as we look at options, record the default option if it exists
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@ -314,15 +335,16 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
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}
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// if their argument has no value (null), and there's a default, return that default for the enum value
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if (defaultEnumeration != null && value == null)
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return defaultEnumeration;
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result = defaultEnumeration;
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// if their argument has no value and there's no default, throw a missing argument value exception.
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// TODO: Clean this up so that null values never make it to this point. To fix this, we'll have to clean up the implementation of -U.
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if (value == null)
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else if (value == null)
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throw new MissingArgumentValueException(Collections.singleton(createDefaultArgumentDefinition(source)));
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throw new UnknownEnumeratedValueException(createDefaultArgumentDefinition(source),value);
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else
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throw new UnknownEnumeratedValueException(createDefaultArgumentDefinition(source),value);
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} else {
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Constructor ctor = type.getConstructor(String.class);
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return ctor.newInstance(value);
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result = ctor.newInstance(value);
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}
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}
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catch (NoSuchMethodException e) {
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@ -334,7 +356,10 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
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} catch (InstantiationException e) {
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throw new StingException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
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}
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// WARNING: Side effect!
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parsingEngine.addTags(result,tags);
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return result;
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}
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@ -367,9 +392,10 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
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@Override
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@SuppressWarnings("unchecked")
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public Object parse( ArgumentSource source, Class type, ArgumentMatches matches )
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{
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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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Set<String> tags = new LinkedHashSet<String>();
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if( Collection.class.isAssignableFrom(type) ) {
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@ -399,11 +425,13 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
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}
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for( ArgumentMatch match: matches ) {
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for( ArgumentMatch value: match )
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collection.add( componentArgumentParser.parse(source,componentType,new ArgumentMatches(value)) );
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for( ArgumentMatch value: match ) {
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collection.add( componentArgumentParser.parse(parsingEngine,source,componentType,new ArgumentMatches(value)) );
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tags.addAll(value.tags);
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}
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}
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return collection;
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result = collection;
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}
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else if( type.isArray() ) {
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@ -412,21 +440,25 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
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// Assemble a collection of individual values used in this computation.
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Collection<ArgumentMatch> values = new ArrayList<ArgumentMatch>();
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for( ArgumentMatch match: matches ) {
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for( ArgumentMatch match: matches )
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for( ArgumentMatch value: match )
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values.add(value);
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}
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Object arr = Array.newInstance(componentType,values.size());
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result = Array.newInstance(componentType,values.size());
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int i = 0;
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for( ArgumentMatch value: values )
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Array.set( arr,i++,componentArgumentParser.parse(source,componentType,new ArgumentMatches(value)));
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return arr;
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for( ArgumentMatch value: values ) {
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Array.set( result,i++,componentArgumentParser.parse(parsingEngine,source,componentType,new ArgumentMatches(value)));
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tags.addAll(value.tags);
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}
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}
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else
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throw new StingException("Unsupported compound argument type: " + type);
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// WARNING: Side effect!
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parsingEngine.addTags(result,new ArrayList<String>(tags));
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return result;
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}
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/**
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@ -506,17 +538,22 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
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@Override
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public Object parse( ArgumentSource source, Class type, ArgumentMatches matches ) {
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public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches) {
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if(multiplexedIds == null)
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throw new StingException("Cannot directly parse a MultiplexArgumentTypeDescriptor; must create a derivative type descriptor first.");
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Map<Object,Object> multiplexedMapping = new HashMap<Object,Object>();
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Class componentType = getCollectionComponentType(source.field);
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for(Object id: multiplexedIds) {
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Object value = ArgumentTypeDescriptor.create(componentType).parse(source,componentType,matches.transform(multiplexer,id));
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Object value = ArgumentTypeDescriptor.create(componentType).parse(parsingEngine,source,componentType,matches.transform(multiplexer,id));
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multiplexedMapping.put(id,value);
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}
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parsingEngine.addTags(multiplexedMapping,getArgumentTags(matches));
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return multiplexedMapping;
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}
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@ -124,6 +124,19 @@ public abstract class CommandLineProgram {
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*/
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protected String getArgumentSourceName( Class source ) { return source.toString(); }
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/**
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* The command-line argument system allows free-form String tags to accompany each
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* object. However, there's no way for the clp to push these tags into the fields
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* themselves, so we just provide a callback so that the clp can push tags into the
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* argument system.
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* @param key Key to use, created by the command-line argument system.
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* @param tags List of freeform tags.
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*/
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protected void addTags(Object key, List<String> tags) {
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// NO-OP by default.
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}
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/**
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* this is the function that the inheriting class can expect to have called
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* when all the argument processing is done
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@ -276,6 +276,15 @@ public class ParsingEngine {
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}
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}
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/**
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* Notify the user that tags have been created.
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* @param key The key created.
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* @param tags List of tags, or empty list if no tags are present.
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*/
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public void addTags(Object key, List<String> tags) {
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if(clp!=null) clp.addTags(key,tags);
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}
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/**
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* Notify the user that a deprecated command-line argument has been used.
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* @param argumentSource Deprecated argument source specified by user.
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@ -308,7 +317,8 @@ public class ParsingEngine {
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throw new StingException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches);
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for( Object target: targets ) {
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Object value = (argumentMatches.size() != 0) ? source.parse(argumentMatches) : source.createDefault();
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Object value = (argumentMatches.size() != 0) ? source.parse(this,argumentMatches) : source.createDefault();
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JVMUtils.setFieldValue(source.field,target,value);
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}
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}
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@ -25,8 +25,12 @@
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package org.broadinstitute.sting.commandline;
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import org.broadinstitute.sting.utils.Utils;
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import java.util.regex.Pattern;
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import java.util.regex.Matcher;
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import java.util.List;
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import java.util.ArrayList;
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/**
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* Holds a pattern, along with how to get to the argument definitions that could match that pattern.
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@ -76,18 +80,32 @@ public abstract class ParsingMethod {
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String argument = matcher.group(1).trim();
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List<String> tags = new ArrayList<String>();
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if(matcher.group(2) != null)
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tags.addAll(Utils.split(matcher.group(2),","));
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// Find the most appropriate argument definition for the given argument.
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ArgumentDefinition argumentDefinition = definitions.findArgumentDefinition( argument, definitionMatcher );
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// Try to find a matching argument. If found, label that as the match. If not found, add the argument
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// with a null definition.
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ArgumentMatch argumentMatch = new ArgumentMatch( argument, argumentDefinition, position );
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ArgumentMatch argumentMatch = new ArgumentMatch( argument, argumentDefinition, position, tags );
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return argumentMatch;
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}
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public static ParsingMethod FullNameParsingMethod = new ParsingMethod(Pattern.compile("\\s*--([A-Za-z_][\\w\\-\\.]*)\\s*"),
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/**
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* A command-line argument always starts with an alphabetical character or underscore followed by any word character.
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*/
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private static final String ARGUMENT_TEXT = "[A-Za-z_][\\w\\-\\.]*";
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/**
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* Tags, on the other hand, can start with any word character.
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*/
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private static final String TAG_TEXT = "[\\w\\-\\.]*";
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public static ParsingMethod FullNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*--(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)),
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ArgumentDefinitions.FullNameDefinitionMatcher) {};
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public static ParsingMethod ShortNameParsingMethod = new ParsingMethod(Pattern.compile("\\s*-([A-Za-z_][\\w\\-]*)\\s*"),
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public static ParsingMethod ShortNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*-(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)),
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ArgumentDefinitions.ShortNameDefinitionMatcher) {};
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}
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|
|
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|
@ -82,12 +82,8 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
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for(SamRecordFilter filter: filters)
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loadArgumentsIntoObject(filter);
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// process any arguments that need a second pass
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GATKArgumentCollection arguments = getArgumentCollection();
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processArguments(arguments);
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|
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// set the analysis name in the argument collection
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return GATKEngine.execute(arguments, mWalker, filters);
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return GATKEngine.execute(getArgumentCollection(), mWalker, filters);
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}
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/**
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@ -133,50 +129,15 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
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@Override
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protected String getArgumentSourceName( Class argumentSource ) {
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return GATKEngine.getWalkerName((Class<Walker>)argumentSource);
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}
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|
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/**
|
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* Preprocess the arguments before submitting them to the GATK engine.
|
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*
|
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* @param argCollection Collection of arguments to preprocess.
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*/
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private void processArguments( GATKArgumentCollection argCollection ) {
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argCollection.samFiles = unpackBAMFileList( argCollection.samFiles );
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}
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/**
|
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* Unpack the bam files to be processed, given a list of files. That list of files can
|
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* itself contain entries which are lists of other files to be read (note: you cannot have lists of lists of lists)
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*
|
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* @param inputFiles a list of files that represent either bam files themselves, or a file containing a list of bam files to process
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*
|
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* @return a flattened list of the bam files provided
|
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* Supply command-line argument tags to the GATK engine.
|
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* @param key Key to use, created by the command-line argument system.
|
||||
* @param tags List of freeform tags.
|
||||
*/
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public static List<File> unpackBAMFileList( List<File> inputFiles ) {
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List<File> unpackedReads = new ArrayList<File>();
|
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for( File inputFile: inputFiles ) {
|
||||
if (inputFile.getName().toLowerCase().endsWith(".list") ) {
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||||
try {
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for(String fileName : new XReadLines(inputFile))
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unpackedReads.addAll(Collections.singletonList(new File(fileName)));
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}
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catch( FileNotFoundException ex ) {
|
||||
throw new StingException("Unable to find file while unpacking reads", ex);
|
||||
}
|
||||
}
|
||||
else if(inputFile.getName().toLowerCase().endsWith(".bam")) {
|
||||
unpackedReads.add( inputFile );
|
||||
}
|
||||
else if(inputFile.getName().equals("-")) {
|
||||
unpackedReads.add( new File("/dev/stdin") );
|
||||
}
|
||||
else {
|
||||
Utils.scareUser(String.format("The GATK reads argument (-I) supports only BAM files with the .bam extension and lists of BAM files " +
|
||||
"with the .list extension, but the file %s has neither extension. Please ensure that your BAM file or list " +
|
||||
"of BAM files is in the correct format, update the extension, and try again.",inputFile.getName()));
|
||||
}
|
||||
}
|
||||
return unpackedReads;
|
||||
@Override
|
||||
protected void addTags(Object key, List<String> tags) {
|
||||
GATKEngine.addTags(key,tags);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -50,11 +50,13 @@ import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackManager;
|
|||
import org.broadinstitute.sting.gatk.refdata.utils.RMDIntervalGenerator;
|
||||
import org.broadinstitute.sting.gatk.walkers.*;
|
||||
import org.broadinstitute.sting.utils.*;
|
||||
import org.broadinstitute.sting.utils.text.XReadLines;
|
||||
import org.broadinstitute.sting.commandline.ArgumentException;
|
||||
import org.broadinstitute.sting.commandline.ArgumentSource;
|
||||
import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.util.*;
|
||||
|
||||
public class GenomeAnalysisEngine {
|
||||
|
|
@ -96,6 +98,11 @@ public class GenomeAnalysisEngine {
|
|||
*/
|
||||
private Collection<Stub<?>> outputs = new ArrayList<Stub<?>>();
|
||||
|
||||
/**
|
||||
* List of tags associated with the given instantiation of the command-line argument.
|
||||
*/
|
||||
private final Map<Object,List<String>> tags = new IdentityHashMap<Object,List<String>>();
|
||||
|
||||
/**
|
||||
* Collection of the filters applied to the walker's input data.
|
||||
*/
|
||||
|
|
@ -280,6 +287,27 @@ public class GenomeAnalysisEngine {
|
|||
outputs.add(stub);
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds an association between a object created by the
|
||||
* command-line argument system and a freeform list of tags.
|
||||
* @param key Object created by the command-line argument system.
|
||||
* @param tags List of tags to use when reading arguments.
|
||||
*/
|
||||
public void addTags(Object key, List<String> tags) {
|
||||
this.tags.put(key,tags);
|
||||
}
|
||||
|
||||
/**
|
||||
* Gets the tags associated with a given object.
|
||||
* @param key Key for which to find a tag.
|
||||
* @return List of tags associated with this key.
|
||||
*/
|
||||
public List<String> getTags(Object key) {
|
||||
if(!tags.containsKey(key))
|
||||
return Collections.emptyList();
|
||||
return tags.get(key);
|
||||
}
|
||||
|
||||
/**
|
||||
* Retrieves an instance of the walker based on the walker name.
|
||||
*
|
||||
|
|
@ -348,7 +376,7 @@ public class GenomeAnalysisEngine {
|
|||
}
|
||||
|
||||
RMDTrackManager manager = new RMDTrackManager();
|
||||
List<RMDTrack> tracks = manager.getReferenceMetaDataSources(argCollection.RODBindings);
|
||||
List<RMDTrack> tracks = manager.getReferenceMetaDataSources(this,argCollection.RODBindings);
|
||||
validateSuppliedReferenceOrderedDataAgainstWalker(my_walker, tracks);
|
||||
|
||||
// validate all the sequence dictionaries against the reference
|
||||
|
|
@ -547,7 +575,7 @@ public class GenomeAnalysisEngine {
|
|||
else
|
||||
method = new DownsamplingMethod(DownsampleType.NONE,null,null);
|
||||
|
||||
return new ReadProperties(argCollection.samFiles,
|
||||
return new ReadProperties(unpackBAMFileList(argCollection.samFiles),
|
||||
argCollection.strictnessLevel,
|
||||
argCollection.readBufferSize,
|
||||
method,
|
||||
|
|
@ -947,4 +975,39 @@ public class GenomeAnalysisEngine {
|
|||
public ReadMetrics getCumulativeMetrics() {
|
||||
return readsDataSource.getCumulativeReadMetrics();
|
||||
}
|
||||
|
||||
/**
|
||||
* Unpack the bam files to be processed, given a list of files. That list of files can
|
||||
* itself contain entries which are lists of other files to be read (note: you cannot have lists of lists of lists)
|
||||
*
|
||||
* @param inputFiles a list of files that represent either bam files themselves, or a file containing a list of bam files to process
|
||||
*
|
||||
* @return a flattened list of the bam files provided
|
||||
*/
|
||||
private List<SAMReaderID> unpackBAMFileList( List<File> inputFiles ) {
|
||||
List<SAMReaderID> unpackedReads = new ArrayList<SAMReaderID>();
|
||||
for( File inputFile: inputFiles ) {
|
||||
if (inputFile.getName().toLowerCase().endsWith(".list") ) {
|
||||
try {
|
||||
for(String fileName : new XReadLines(inputFile))
|
||||
unpackedReads.add(new SAMReaderID(new File(fileName),getTags(inputFile)));
|
||||
}
|
||||
catch( FileNotFoundException ex ) {
|
||||
throw new StingException("Unable to find file while unpacking reads", ex);
|
||||
}
|
||||
}
|
||||
else if(inputFile.getName().toLowerCase().endsWith(".bam")) {
|
||||
unpackedReads.add( new SAMReaderID(inputFile,getTags(inputFile)) );
|
||||
}
|
||||
else if(inputFile.getName().equals("-")) {
|
||||
unpackedReads.add(new SAMReaderID(new File("/dev/stdin"),Collections.<String>emptyList()));
|
||||
}
|
||||
else {
|
||||
Utils.scareUser(String.format("The GATK reads argument (-I) supports only BAM files with the .bam extension and lists of BAM files " +
|
||||
"with the .list extension, but the file %s has neither extension. Please ensure that your BAM file or list " +
|
||||
"of BAM files is in the correct format, update the extension, and try again.",inputFile.getName()));
|
||||
}
|
||||
}
|
||||
return unpackedReads;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk;
|
|||
import net.sf.picard.filter.SamRecordFilter;
|
||||
import net.sf.samtools.SAMFileReader;
|
||||
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.Collection;
|
||||
|
|
@ -26,7 +26,7 @@ import java.util.Collection;
|
|||
* information about how they should be downsampled, sorted, and filtered.
|
||||
*/
|
||||
public class ReadProperties {
|
||||
private List<File> readsFiles = null;
|
||||
private List<SAMReaderID> readers = null;
|
||||
private SAMFileReader.ValidationStringency validationStringency = SAMFileReader.ValidationStringency.STRICT;
|
||||
private Integer readBufferSize = null;
|
||||
private DownsamplingMethod downsamplingMethod = null;
|
||||
|
|
@ -63,8 +63,8 @@ public class ReadProperties {
|
|||
* Gets a list of the files acting as sources of reads.
|
||||
* @return A list of files storing reads data.
|
||||
*/
|
||||
public List<File> getReadsFiles() {
|
||||
return readsFiles;
|
||||
public List<SAMReaderID> getSAMReaderIDs() {
|
||||
return readers;
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -115,8 +115,8 @@ public class ReadProperties {
|
|||
* Simple constructor for unit testing.
|
||||
* @param readsFiles List of reads files to open.
|
||||
*/
|
||||
public ReadProperties( List<File> readsFiles ) {
|
||||
this.readsFiles = readsFiles;
|
||||
public ReadProperties( List<SAMReaderID> readsFiles ) {
|
||||
this.readers = readsFiles;
|
||||
this.downsamplingMethod = new DownsamplingMethod(DownsampleType.NONE,null,null);
|
||||
this.supplementalFilters = new ArrayList<SamRecordFilter>();
|
||||
this.exclusionList = new ValidationExclusion();
|
||||
|
|
@ -138,7 +138,7 @@ public class ReadProperties {
|
|||
* will explicitly list reads with deletion over the current reference base; otherwise, only observed
|
||||
* bases will be seen in the pileups, and the deletions will be skipped silently.
|
||||
*/
|
||||
ReadProperties( List<File> samFiles,
|
||||
ReadProperties( List<SAMReaderID> samFiles,
|
||||
SAMFileReader.ValidationStringency strictness,
|
||||
Integer readBufferSize,
|
||||
DownsamplingMethod downsamplingMethod,
|
||||
|
|
@ -147,7 +147,7 @@ public class ReadProperties {
|
|||
int maximumReadsAtLocus,
|
||||
boolean includeReadsWithDeletionAtLoci,
|
||||
boolean generateExtendedEvents) {
|
||||
this.readsFiles = samFiles;
|
||||
this.readers = samFiles;
|
||||
this.readBufferSize = readBufferSize;
|
||||
this.validationStringency = strictness;
|
||||
this.downsamplingMethod = downsamplingMethod;
|
||||
|
|
|
|||
|
|
@ -31,6 +31,7 @@ import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
|
|||
import org.broadinstitute.sting.commandline.Argument;
|
||||
import org.broadinstitute.sting.commandline.Input;
|
||||
import org.broadinstitute.sting.gatk.DownsampleType;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
|
||||
import org.broadinstitute.sting.utils.interval.IntervalSetRule;
|
||||
import org.simpleframework.xml.*;
|
||||
import org.simpleframework.xml.core.Persister;
|
||||
|
|
|
|||
|
|
@ -65,7 +65,7 @@ public class SAMDataSource implements SimpleDataSource {
|
|||
/**
|
||||
* Identifiers for the readers driving this data source.
|
||||
*/
|
||||
protected final List<SAMReaderID> readerIDs = new ArrayList<SAMReaderID>();
|
||||
protected final List<SAMReaderID> readerIDs;
|
||||
|
||||
/**
|
||||
* How far along is each reader?
|
||||
|
|
@ -109,11 +109,10 @@ public class SAMDataSource implements SimpleDataSource {
|
|||
this.readProperties = reads;
|
||||
this.readMetrics = new ReadMetrics();
|
||||
|
||||
for (File smFile : reads.getReadsFiles()) {
|
||||
if (!smFile.canRead()) {
|
||||
throw new SimpleDataSourceLoadException("SAMDataSource: Unable to load file: " + smFile.getName());
|
||||
}
|
||||
readerIDs.add(new SAMReaderID(smFile));
|
||||
readerIDs = reads.getSAMReaderIDs();
|
||||
for (SAMReaderID readerID : reads.getSAMReaderIDs()) {
|
||||
if (!readerID.samFile.canRead())
|
||||
throw new SimpleDataSourceLoadException("SAMDataSource: Unable to load file: " + readerID.samFile.getName());
|
||||
}
|
||||
|
||||
resourcePool = new SAMResourcePool(Integer.MAX_VALUE);
|
||||
|
|
@ -170,7 +169,7 @@ public class SAMDataSource implements SimpleDataSource {
|
|||
* @return True if no reads files are supplying data to the traversal; false otherwise.
|
||||
*/
|
||||
public boolean isEmpty() {
|
||||
return readProperties.getReadsFiles().size() == 0;
|
||||
return readProperties.getSAMReaderIDs().size() == 0;
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -550,8 +549,8 @@ public class SAMDataSource implements SimpleDataSource {
|
|||
* @param sourceInfo Metadata for the reads to load.
|
||||
*/
|
||||
public SAMReaders(ReadProperties sourceInfo) {
|
||||
for(File readsFile: sourceInfo.getReadsFiles()) {
|
||||
SAMFileReader reader = new SAMFileReader(readsFile);
|
||||
for(SAMReaderID readerID: sourceInfo.getSAMReaderIDs()) {
|
||||
SAMFileReader reader = new SAMFileReader(readerID.samFile);
|
||||
reader.enableFileSource(true);
|
||||
reader.enableIndexCaching(true);
|
||||
reader.setValidationStringency(sourceInfo.getValidationStringency());
|
||||
|
|
@ -562,14 +561,14 @@ public class SAMDataSource implements SimpleDataSource {
|
|||
logger.debug(String.format("Sort order is: " + header.getSortOrder()));
|
||||
|
||||
if (reader.getFileHeader().getReadGroups().size() < 1) {
|
||||
SAMReadGroupRecord rec = new SAMReadGroupRecord(readsFile.getName());
|
||||
rec.setLibrary(readsFile.getName());
|
||||
rec.setSample(readsFile.getName());
|
||||
SAMReadGroupRecord rec = new SAMReadGroupRecord(readerID.samFile.getName());
|
||||
rec.setLibrary(readerID.samFile.getName());
|
||||
rec.setSample(readerID.samFile.getName());
|
||||
|
||||
reader.getFileHeader().addReadGroup(rec);
|
||||
}
|
||||
|
||||
readers.put(new SAMReaderID(readsFile),reader);
|
||||
readers.put(readerID,reader);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,6 +1,8 @@
|
|||
package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.List;
|
||||
import java.util.Collections;
|
||||
|
||||
/**
|
||||
* Uniquely identifies a SAM file reader.
|
||||
|
|
@ -15,12 +17,27 @@ public class SAMReaderID {
|
|||
*/
|
||||
protected final File samFile;
|
||||
|
||||
/**
|
||||
* A list of tags associated with this BAM file.
|
||||
*/
|
||||
protected final List<String> tags;
|
||||
|
||||
/**
|
||||
* Creates an identifier for a SAM file based on read.
|
||||
* @param samFile The source file for SAM data.
|
||||
* @param tags tags to use when creating a reader ID.
|
||||
*/
|
||||
protected SAMReaderID(File samFile) {
|
||||
public SAMReaderID(File samFile, List<String> tags) {
|
||||
this.samFile = samFile;
|
||||
this.tags = tags;
|
||||
}
|
||||
|
||||
/**
|
||||
* Gets the tags associated with the given BAM file.
|
||||
* @return A collection of the tags associated with this file.
|
||||
*/
|
||||
public List<String> getTags() {
|
||||
return Collections.unmodifiableList(tags);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -30,6 +30,7 @@ import org.broadinstitute.sting.gatk.datasources.shards.Shard;
|
|||
import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
|
||||
import org.broadinstitute.sting.gatk.traversals.*;
|
||||
import org.broadinstitute.sting.gatk.walkers.*;
|
||||
import org.broadinstitute.sting.gatk.io.OutputTracker;
|
||||
|
|
@ -147,7 +148,7 @@ public abstract class MicroScheduler {
|
|||
* @return an iterator over the reads specified in the shard.
|
||||
*/
|
||||
protected StingSAMIterator getReadIterator(Shard shard) {
|
||||
return (!reads.isEmpty()) ? reads.seek(shard) : new NullSAMIterator(new ReadProperties(new ArrayList<File>()));
|
||||
return (!reads.isEmpty()) ? reads.seek(shard) : new NullSAMIterator(new ReadProperties(Collections.<SAMReaderID>emptyList()));
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -77,7 +77,7 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
|
|||
}
|
||||
|
||||
@Override
|
||||
public Object parse( ArgumentSource source, Class type, ArgumentMatches matches ) {
|
||||
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches ) {
|
||||
ArgumentDefinition definition = createDefaultArgumentDefinition(source);
|
||||
String fileName = getArgumentValue( definition, matches );
|
||||
|
||||
|
|
@ -85,7 +85,11 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
|
|||
|
||||
engine.addOutput(stub);
|
||||
|
||||
return createInstanceOfClass(type,stub);
|
||||
Object result = createInstanceOfClass(type,stub);
|
||||
// WARNING: Side effects required by engine!
|
||||
parsingEngine.addTags(result,getArgumentTags(matches));
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.io.stubs;
|
|||
import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
|
||||
import org.broadinstitute.sting.commandline.ArgumentSource;
|
||||
import org.broadinstitute.sting.commandline.ArgumentMatches;
|
||||
import org.broadinstitute.sting.commandline.ParsingEngine;
|
||||
import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
|
||||
|
|
@ -59,7 +60,7 @@ public class SAMFileReaderArgumentTypeDescriptor extends ArgumentTypeDescriptor
|
|||
}
|
||||
|
||||
@Override
|
||||
public Object parse( ArgumentSource source, Class type, ArgumentMatches matches ) {
|
||||
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches ) {
|
||||
SAMFileReaderBuilder builder = new SAMFileReaderBuilder();
|
||||
|
||||
String readerFileName = getArgumentValue( createDefaultArgumentDefinition(source), matches );
|
||||
|
|
@ -69,6 +70,7 @@ public class SAMFileReaderArgumentTypeDescriptor extends ArgumentTypeDescriptor
|
|||
|
||||
builder.setSAMFile(new File(readerFileName));
|
||||
|
||||
// WARNING: Skipping required side-effect because stub is impossible to generate.
|
||||
engine.addInput(source, builder);
|
||||
|
||||
// MASSIVE KLUDGE! SAMFileReader is tricky to implement and we don't yet have a stub. Return null, then
|
||||
|
|
|
|||
|
|
@ -91,7 +91,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
|
|||
}
|
||||
|
||||
@Override
|
||||
public Object parse( ArgumentSource source, Class type, ArgumentMatches matches ) {
|
||||
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches ) {
|
||||
String writerFileName = getArgumentValue( createBAMArgumentDefinition(source), matches );
|
||||
if( writerFileName == null )
|
||||
throw new StingException("SAM file compression was supplied, but no associated writer was supplied with it.");
|
||||
|
|
@ -103,6 +103,8 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
|
|||
if( compressionLevel != null )
|
||||
stub.setCompressionLevel(compressionLevel);
|
||||
|
||||
// WARNING: Side effects required by engine!
|
||||
parsingEngine.addTags(stub,getArgumentTags(matches));
|
||||
engine.addOutput(stub);
|
||||
|
||||
return stub;
|
||||
|
|
@ -121,7 +123,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
|
|||
DEFAULT_ARGUMENT_FULLNAME,
|
||||
DEFAULT_ARGUMENT_SHORTNAME,
|
||||
ArgumentDefinition.getDoc(annotation),
|
||||
true,
|
||||
false,
|
||||
false,
|
||||
source.isMultiValued(),
|
||||
source.isHidden(),
|
||||
|
|
|
|||
|
|
@ -111,7 +111,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
|
|||
* @return Transform from the matches into the associated argument.
|
||||
*/
|
||||
@Override
|
||||
public Object parse( ArgumentSource source, Class type, ArgumentMatches matches ) {
|
||||
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches ) {
|
||||
// Get the filename for the genotype file, if it exists. If not, we'll need to send output to out.
|
||||
String writerFileName = getArgumentValue(createDefaultArgumentDefinition(source),matches);
|
||||
File writerFile = writerFileName != null ? new File(writerFileName) : null;
|
||||
|
|
@ -122,6 +122,8 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
|
|||
// Create a stub for the given object.
|
||||
VCFWriterStub stub = (writerFile != null) ? new VCFWriterStub(engine, writerFile, compress) : new VCFWriterStub(engine, System.out, compress);
|
||||
|
||||
// WARNING: Side effects required by engine!
|
||||
parsingEngine.addTags(stub,getArgumentTags(matches));
|
||||
engine.addOutput(stub);
|
||||
|
||||
return stub;
|
||||
|
|
|
|||
|
|
@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.refdata.tracks;
|
|||
|
||||
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
|
||||
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
|
||||
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
|
||||
import org.broadinstitute.sting.utils.classloader.PluginManager;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
|
||||
|
|
@ -62,13 +63,13 @@ public class RMDTrackManager extends PluginManager<RMDTrackBuilder> {
|
|||
/**
|
||||
* find the associated reference meta data
|
||||
*
|
||||
* @param triplets the triplets of strings from the -B command line option
|
||||
* @param bindings the bindings of strings from the -B command line option
|
||||
*
|
||||
* @return a list of RMDTracks, one for each -B option
|
||||
*/
|
||||
public List<RMDTrack> getReferenceMetaDataSources(List<String> triplets) {
|
||||
public List<RMDTrack> getReferenceMetaDataSources(GenomeAnalysisEngine engine,List<String> bindings) {
|
||||
initializeTrackTypes();
|
||||
initializeTriplets(triplets);
|
||||
initializeBindings(engine,bindings);
|
||||
// try and make the tracks given their requests
|
||||
return createRequestedTrackObjects();
|
||||
}
|
||||
|
|
@ -91,18 +92,30 @@ public class RMDTrackManager extends PluginManager<RMDTrackBuilder> {
|
|||
}
|
||||
|
||||
/**
|
||||
* initialize our lists of triplets
|
||||
* @param triplets the input to the GATK, as a list of strings passed in through the -B options
|
||||
* initialize our lists of bindings
|
||||
* @param engine The engine, used to populate tags.
|
||||
* @param bindings the input to the GATK, as a list of strings passed in through the -B options
|
||||
*/
|
||||
private void initializeTriplets(List<String> triplets) {
|
||||
private void initializeBindings(GenomeAnalysisEngine engine,List<String> bindings) {
|
||||
// NOTE: Method acts as a static. Once the inputs have been passed once they are locked in.
|
||||
if (inputs.size() > 0 || triplets.size() == 0)
|
||||
if (inputs.size() > 0 || bindings.size() == 0)
|
||||
return;
|
||||
|
||||
for (String value: triplets) {
|
||||
String[] split = value.split(",");
|
||||
if (split.length != 3) throw new IllegalArgumentException(value + " is not a valid reference metadata track description");
|
||||
inputs.add(new RMDTriplet(split[0], split[1], split[2]));
|
||||
for (String binding: bindings) {
|
||||
if(engine != null && engine.getTags(binding).size() == 2) {
|
||||
// Assume that if tags are present, those tags are name and type.
|
||||
// Name is always first, followed by type.
|
||||
List<String> parameters = engine.getTags(binding);
|
||||
String name = parameters.get(0);
|
||||
String type = parameters.get(1);
|
||||
inputs.add(new RMDTriplet(name,type,binding));
|
||||
}
|
||||
else {
|
||||
// Otherwise, use old-format bindings.
|
||||
String[] split = binding.split(",");
|
||||
if (split.length != 3) throw new IllegalArgumentException(binding + " is not a valid reference metadata track description");
|
||||
inputs.add(new RMDTriplet(split[0], split[1], split[2]));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@ import java.io.PrintStream;
|
|||
@Requires({DataSource.READS, DataSource.REFERENCE})
|
||||
public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
|
||||
/** an optional argument to dump the reads out to a BAM file */
|
||||
@Output(doc="Write output to this BAM filename instead of STDOUT",required=false)
|
||||
@Output(doc="Write output to this BAM filename instead of STDOUT")
|
||||
SAMFileWriter out;
|
||||
@Argument(fullName = "readGroup", shortName = "readGroup", doc="Discard reads not belonging to the specified read group", required = false)
|
||||
String readGroup = null;
|
||||
|
|
|
|||
|
|
@ -19,7 +19,6 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
|
|||
import org.junit.BeforeClass;
|
||||
import org.junit.Test;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.util.*;
|
||||
/**
|
||||
|
|
@ -51,7 +50,7 @@ public abstract class LocusViewTemplate extends BaseTest {
|
|||
SAMRecordIterator iterator = new SAMRecordIterator();
|
||||
|
||||
GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1", 1, 5);
|
||||
Shard shard = new LocusShard(new SAMDataSource(new ReadProperties(Collections.<File>emptyList())),Collections.singletonList(shardBounds),Collections.<SAMReaderID,SAMFileSpan>emptyMap());
|
||||
Shard shard = new LocusShard(new SAMDataSource(new ReadProperties(Collections.<SAMReaderID>emptyList())),Collections.singletonList(shardBounds),Collections.<SAMReaderID,SAMFileSpan>emptyMap());
|
||||
WindowMaker windowMaker = new WindowMaker(shard,iterator,shard.getGenomeLocs(),LocusIteratorByState.NO_FILTERS);
|
||||
WindowMaker.WindowMakerIterator window = windowMaker.next();
|
||||
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, window.getLocus(), window, null, null);
|
||||
|
|
|
|||
|
|
@ -27,10 +27,10 @@ package org.broadinstitute.sting.gatk.datasources.shards;
|
|||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.gatk.ReadProperties;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Collections;
|
||||
import java.io.File;
|
||||
|
||||
/**
|
||||
* A mock locus shard, usable for infrastructure that requires a shard to behave properly.
|
||||
|
|
@ -40,6 +40,6 @@ import java.io.File;
|
|||
*/
|
||||
public class MockLocusShard extends LocusShard {
|
||||
public MockLocusShard(final List<GenomeLoc> intervals) {
|
||||
super(new SAMDataSource(new ReadProperties(Collections.<File>emptyList())),intervals,null);
|
||||
super(new SAMDataSource(new ReadProperties(Collections.<SAMReaderID>emptyList())),intervals,null);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -19,6 +19,7 @@ import java.io.File;
|
|||
import java.io.FileNotFoundException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.Collections;
|
||||
|
||||
/**
|
||||
*
|
||||
|
|
@ -48,7 +49,7 @@ import java.util.List;
|
|||
*/
|
||||
public class SAMBAMDataSourceUnitTest extends BaseTest {
|
||||
|
||||
private List<File> fl;
|
||||
private List<SAMReaderID> readers;
|
||||
private IndexedFastaSequenceFile seq;
|
||||
|
||||
/**
|
||||
|
|
@ -58,7 +59,7 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
|
|||
*/
|
||||
@Before
|
||||
public void doForEachTest() throws FileNotFoundException {
|
||||
fl = new ArrayList<File>();
|
||||
readers = new ArrayList<SAMReaderID>();
|
||||
|
||||
// sequence
|
||||
seq = new IndexedFastaSequenceFile(new File(hg18Reference));
|
||||
|
|
@ -73,7 +74,7 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
|
|||
@After
|
||||
public void undoForEachTest() {
|
||||
seq = null;
|
||||
fl.clear();
|
||||
readers.clear();
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -83,8 +84,8 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
|
|||
logger.warn("Executing testLinearBreakIterateAll");
|
||||
|
||||
// setup the data
|
||||
fl.add(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"));
|
||||
ReadProperties reads = new ReadProperties(fl);
|
||||
readers.add(new SAMReaderID(new File(validationDataLocation+"/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
|
||||
ReadProperties reads = new ReadProperties(readers);
|
||||
|
||||
// the sharding strat.
|
||||
SAMDataSource data = new SAMDataSource(reads);
|
||||
|
|
@ -128,8 +129,8 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
|
|||
logger.warn("Executing testMergingTwoBAMFiles");
|
||||
|
||||
// setup the test files
|
||||
fl.add(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"));
|
||||
ReadProperties reads = new ReadProperties(fl);
|
||||
readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
|
||||
ReadProperties reads = new ReadProperties(readers);
|
||||
|
||||
// the sharding strat.
|
||||
SAMDataSource data = new SAMDataSource(reads);
|
||||
|
|
@ -168,10 +169,10 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
|
|||
|
||||
|
||||
// setup the data and the counter before our second run
|
||||
fl.clear();
|
||||
fl.add(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"));
|
||||
fl.add(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"));
|
||||
reads = new ReadProperties(fl);
|
||||
readers.clear();
|
||||
readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
|
||||
readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
|
||||
reads = new ReadProperties(readers);
|
||||
|
||||
count = 0;
|
||||
// the sharding strat.
|
||||
|
|
|
|||
|
|
@ -6,6 +6,7 @@ import net.sf.samtools.SAMRecord;
|
|||
import net.sf.samtools.util.CloseableIterator;
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.broadinstitute.sting.gatk.ReadProperties;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.utils.GenomeLocParser;
|
||||
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
|
||||
|
|
@ -40,7 +41,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
|
|||
final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
|
||||
|
||||
// create a test version of the Reads object
|
||||
ReadProperties readAttributes = new ReadProperties(new ArrayList<File>());
|
||||
ReadProperties readAttributes = new ReadProperties(new ArrayList<SAMReaderID>());
|
||||
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
|
||||
|
||||
SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
|
||||
|
|
@ -92,7 +93,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
|
|||
final byte[] quals = new byte[] { 20, 20, 20, 20, 20, 20, 20, 20, 20, 20};
|
||||
|
||||
// create a test version of the Reads object
|
||||
ReadProperties readAttributes = new ReadProperties(new ArrayList<File>());
|
||||
ReadProperties readAttributes = new ReadProperties(new ArrayList<SAMReaderID>());
|
||||
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
|
||||
|
||||
SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
|
||||
|
|
@ -140,7 +141,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
|
|||
records.add(ArtificialSAMUtils.createArtificialRead(header, "readUno", 0, x, 20));
|
||||
|
||||
// create a test version of the Reads object
|
||||
ReadProperties reads = new ReadProperties(new ArrayList<File>());
|
||||
ReadProperties reads = new ReadProperties(new ArrayList<SAMReaderID>());
|
||||
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"maximumReadsAtLocus"),reads,MAX_READS);
|
||||
|
||||
// create the iterator by state with the fake reads and fake records
|
||||
|
|
@ -166,7 +167,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
|
|||
records.add(ArtificialSAMUtils.createArtificialRead(header, "readUno", 0, 100, 20));
|
||||
|
||||
// create a test version of the Reads object
|
||||
ReadProperties reads = new ReadProperties(new ArrayList<File>());
|
||||
ReadProperties reads = new ReadProperties(new ArrayList<SAMReaderID>());
|
||||
JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"maximumReadsAtLocus"),reads,MAX_READS);
|
||||
|
||||
// create the iterator by state with the fake reads and fake records
|
||||
|
|
|
|||
|
|
@ -108,8 +108,8 @@ public class RMDTrackManagerUnitTest extends BaseTest {
|
|||
triplets.add("db");
|
||||
triplets.add("DBSNP");
|
||||
triplets.add("../../GATK_Data/dbsnp_130_b36.rod");
|
||||
Assert.assertEquals(1, manager.getReferenceMetaDataSources(triplets).size());
|
||||
RMDTrack t = manager.getReferenceMetaDataSources(triplets).get(0);
|
||||
Assert.assertEquals(1, manager.getReferenceMetaDataSources(null,triplets).size());
|
||||
RMDTrack t = manager.getReferenceMetaDataSources(null,triplets).get(0);
|
||||
// make sure we have a single track
|
||||
// lets test the first and 20th contigs of the human reference
|
||||
|
||||
|
|
|
|||
|
|
@ -11,6 +11,7 @@ import org.broadinstitute.sting.gatk.datasources.shards.Shard;
|
|||
import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy;
|
||||
import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
|
||||
import org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker;
|
||||
import org.broadinstitute.sting.gatk.walkers.Walker;
|
||||
import org.broadinstitute.sting.utils.GenomeLocParser;
|
||||
|
|
@ -56,9 +57,9 @@ import java.util.Collections;
|
|||
public class TraverseReadsUnitTest extends BaseTest {
|
||||
|
||||
private ReferenceSequenceFile seq;
|
||||
private File bam = new File(validationDataLocation + "index_test.bam"); // TCGA-06-0188.aligned.duplicates_marked.bam");
|
||||
private SAMReaderID bam = new SAMReaderID(new File(validationDataLocation + "index_test.bam"),Collections.<String>emptyList()); // TCGA-06-0188.aligned.duplicates_marked.bam");
|
||||
private File refFile = new File(validationDataLocation + "Homo_sapiens_assembly17.fasta");
|
||||
private List<File> bamList;
|
||||
private List<SAMReaderID> bamList;
|
||||
private Walker countReadWalker;
|
||||
private File output;
|
||||
private long readSize = 100000;
|
||||
|
|
@ -82,7 +83,7 @@ public class TraverseReadsUnitTest extends BaseTest {
|
|||
fail("Couldn't open the output file");
|
||||
}
|
||||
|
||||
bamList = new ArrayList<File>();
|
||||
bamList = new ArrayList<SAMReaderID>();
|
||||
bamList.add(bam);
|
||||
countReadWalker = new CountReadsWalker();
|
||||
|
||||
|
|
|
|||
|
|
@ -14,13 +14,13 @@ public class
|
|||
|
||||
private static String root = cmdRoot +
|
||||
" -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
|
||||
" -B eval,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
|
||||
" -B comp_genotypes,VCF," + validationDataLocation + "yri.trio.gatk.ug.head.vcf -reportType Grep";
|
||||
" -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
|
||||
" -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf -reportType Grep";
|
||||
|
||||
private static String rootGZ = cmdRoot +
|
||||
" -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
|
||||
" -B eval,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" +
|
||||
" -B comp_genotypes,VCF," + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz -reportType Grep";
|
||||
" -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" +
|
||||
" -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz -reportType Grep";
|
||||
|
||||
private static String[] testsEnumerations = {root, rootGZ};
|
||||
|
||||
|
|
@ -46,7 +46,7 @@ public class
|
|||
public void testVEGenotypeConcordance() {
|
||||
String vcfFiles[] = {"GenotypeConcordanceEval.vcf", "GenotypeConcordanceEval.vcf.gz"};
|
||||
for (String vcfFile : vcfFiles) {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B eval,VCF," + validationDataLocation + vcfFile + " -B comp,VCF," + validationDataLocation + "GenotypeConcordanceComp.vcf -noStandard -E GenotypeConcordance -reportType CSV -o %s",
|
||||
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noStandard -E GenotypeConcordance -reportType CSV -o %s",
|
||||
1,
|
||||
Arrays.asList("15d1075d384da2bb7445f7493f2b6a07"));
|
||||
executeTest("testVEGenotypeConcordance" + vcfFile, spec);
|
||||
|
|
@ -76,8 +76,8 @@ public class
|
|||
public void testVEComplex() {
|
||||
HashMap<String, String> expectations = new HashMap<String, String>();
|
||||
String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -MVQ 30 -E MendelianViolationEvaluator" +
|
||||
" -B dbsnp_130,dbSNP," + GATKDataLocation + "dbsnp_130_b36.rod" +
|
||||
" -B comp_hapmap,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
|
||||
" -B:dbsnp_130,dbSNP " + GATKDataLocation + "dbsnp_130_b36.rod" +
|
||||
" -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
|
||||
|
||||
|
||||
String matchingMD5 = "dd513bc72860133a58e9ee542782162b";
|
||||
|
|
@ -104,7 +104,7 @@ public class
|
|||
" -L 21" +
|
||||
" -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
|
||||
" -E CountFunctionalClasses -noStandard" +
|
||||
" -B eval,VCF," + validationDataLocation + "test.filtered.maf_annotated.vcf" +
|
||||
" -B:eval,VCF " + validationDataLocation + "test.filtered.maf_annotated.vcf" +
|
||||
" -o %s";
|
||||
String md5 = "d41d8cd98f00b204e9800998ecf8427e";
|
||||
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@ package org.broadinstitute.sting.queue.util
|
|||
import collection.JavaConversions._
|
||||
import org.broadinstitute.sting.queue.QException
|
||||
import java.lang.Class
|
||||
import org.broadinstitute.sting.commandline.{ArgumentMatches, ArgumentSource, ArgumentTypeDescriptor}
|
||||
import org.broadinstitute.sting.commandline.{ArgumentMatches, ArgumentSource, ArgumentTypeDescriptor, ParsingEngine}
|
||||
|
||||
/**
|
||||
* An ArgumentTypeDescriptor that can parse the scala collections.
|
||||
|
|
@ -42,7 +42,7 @@ class ScalaCompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
|
|||
* @param argumentMatches The argument match strings that were found for this argument source.
|
||||
* @return The parsed object.
|
||||
*/
|
||||
def parse(source: ArgumentSource, classType: Class[_], argumentMatches: ArgumentMatches) = {
|
||||
def parse(parsingEngine: ParsingEngine, source: ArgumentSource, classType: Class[_], argumentMatches: ArgumentMatches) = {
|
||||
val componentType = ReflectionUtils.getCollectionType(source.field)
|
||||
val componentArgumentParser = ArgumentTypeDescriptor.create(componentType)
|
||||
|
||||
|
|
@ -50,19 +50,19 @@ class ScalaCompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
|
|||
var list = List.empty[Any]
|
||||
for (argumentMatch <- argumentMatches)
|
||||
for (value <- argumentMatch)
|
||||
list :+= componentArgumentParser.parse(source, componentType, new ArgumentMatches(value))
|
||||
list :+= componentArgumentParser.parse(parsingEngine, source, componentType, new ArgumentMatches(value))
|
||||
list
|
||||
} else if (classOf[Set[_]].isAssignableFrom(classType)) {
|
||||
var set = Set.empty[Any]
|
||||
for (argumentMatch <- argumentMatches)
|
||||
for (value <- argumentMatch)
|
||||
set += componentArgumentParser.parse(source, componentType, new ArgumentMatches(value))
|
||||
set += componentArgumentParser.parse(parsingEngine, source, componentType, new ArgumentMatches(value))
|
||||
set
|
||||
} else if (classOf[Option[_]].isAssignableFrom(classType)) {
|
||||
if (argumentMatches.size > 1)
|
||||
throw new QException("Unable to set Option to multiple values: " + argumentMatches.mkString(" "))
|
||||
else if (argumentMatches.size == 1)
|
||||
Some(componentArgumentParser.parse(source, componentType, argumentMatches))
|
||||
Some(componentArgumentParser.parse(parsingEngine, source, componentType, argumentMatches))
|
||||
else
|
||||
None
|
||||
} else
|
||||
|
|
|
|||
Loading…
Reference in New Issue