/*
* 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.alignment.reference.packing;
import htsjdk.samtools.reference.ReferenceSequence;
import htsjdk.samtools.reference.ReferenceSequenceFile;
import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
import java.io.File;
import java.io.IOException;
/**
* Generate a .PAC file from a given reference.
*
* @author hanna
* @version 0.1
*/
public class CreatePACFromReference {
public static void main( String argv[] ) throws IOException {
if( argv.length != 3 ) {
System.out.println("USAGE: CreatePACFromReference <input>.fasta <output pac> <output rpac>");
return;
}
// Read in the first sequence in the input file
String inputFileName = argv[0];
File inputFile = new File(inputFileName);
ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(inputFile);
ReferenceSequence sequence = reference.nextSequence();
// Target file for output
PackUtils.writeReferenceSequence( new File(argv[1]), sequence.getBases() );
// Reverse the bases in the reference
PackUtils.reverse(sequence.getBases());
// Target file for output
PackUtils.writeReferenceSequence( new File(argv[2]), sequence.getBases() );
}
}