/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.engine.io.stubs;
import htsjdk.samtools.SAMFileReader;
import org.broadinstitute.gatk.utils.commandline.*;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.sam.SAMFileReaderBuilder;
import java.lang.reflect.Type;
/**
* Describe how to parse SAMFileReaders.
*/
public class SAMFileReaderArgumentTypeDescriptor extends ArgumentTypeDescriptor {
/**
* The engine into which output stubs should be fed.
*/
private GenomeAnalysisEngine engine;
/**
* Create a new SAMFileReader argument, notifying the given engine when that argument has been created.
* @param engine engine
*/
public SAMFileReaderArgumentTypeDescriptor( GenomeAnalysisEngine engine ) {
this.engine = engine;
}
@Override
public boolean supports( Class type ) {
return SAMFileReader.class.isAssignableFrom(type);
}
@Override
public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Type type, ArgumentMatches matches ) {
SAMFileReaderBuilder builder = new SAMFileReaderBuilder();
ArgumentMatchValue readerFileName = getArgumentValue( createDefaultArgumentDefinition(source), matches );
if( readerFileName == null )
throw new UserException.CommandLineException("SAM file compression was supplied, but no associated writer was supplied with it.");
builder.setSAMFile(readerFileName.asFile());
// 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
// let the output tracker load it in.
// TODO: Add a stub for SAMFileReader.
return null;
}
}