/*
* 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.utils.sam;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import java.io.File;
/**
* Allows the user to steadily accumulate information about what
* components go into a SAM file writer, ultimately using this
* information to create a SAM file writer on demand.
*
* @author mhanna
* @version 0.1
*/
public class SAMFileReaderBuilder {
/**
* To which file should output be written?
*/
private File samFile = null;
/**
* What compression level should be used when building this file?
*/
private ValidationStringency validationStringency = null;
/**
* Sets the handle of the sam file to which data should be written.
* @param samFile The SAM file into which data should flow.
*/
public void setSAMFile( File samFile ) {
this.samFile = samFile;
}
/**
* Sets the validation stringency to apply when reading this sam file.
* @param validationStringency Stringency to apply. Must not be null.
*/
public void setValidationStringency( ValidationStringency validationStringency ) {
this.validationStringency = validationStringency;
}
/**
* Create the SAM writer, given the constituent parts accrued.
* @return Newly minted SAM file writer.
*/
public SAMFileReader build() {
if( samFile == null )
throw new ReviewedGATKException( "Filename for output sam file must be supplied.");
if( validationStringency == null )
throw new ReviewedGATKException( "Header for output sam file must be supplied.");
SAMFileReader reader = new SAMFileReader( samFile );
reader.setValidationStringency( validationStringency );
return reader;
}
}