143 lines
4.5 KiB
Java
Executable File
143 lines
4.5 KiB
Java
Executable File
/*
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* Copyright (c) 2009 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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*
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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.bwa;
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import org.broadinstitute.sting.utils.StingException;
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import java.io.*;
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/**
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* Write packed bases to an output stream. Pack each base into 2 bits.
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*
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* @author mhanna
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* @version 0.1
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*/
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public class BytePackedOutputStream {
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/**
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* How many possible bases can be encoded?
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*/
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public static final int ALPHABET_SIZE = 4;
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/**
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* Ultimate target for the packed bases.
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*/
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private final OutputStream targetOutputStream;
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/**
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* The next byte to write to the output stream. Will be added
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* to the output stream when enough bases are accumulated, or when
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* the file is closed.
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*/
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private byte packedBases;
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/**
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* Where will the next base be embedded into packedBases?
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*/
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private int positionInPack = 0;
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public BytePackedOutputStream( File outputFile ) throws FileNotFoundException {
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this(new BufferedOutputStream(new FileOutputStream(outputFile)));
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}
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/**
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* Write packed bases to the given output stream.
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* @param outputStream Output stream to which to write packed bases.
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*/
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public BytePackedOutputStream( OutputStream outputStream ) {
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this.targetOutputStream = outputStream;
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}
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/**
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* Write a given base to the output stream.
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* @param base Base to write.
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* @throws IOException if an I/O error occurs.
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*/
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public void write( byte base ) throws IOException {
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packedBases |= (getPackedRepresentation(base) << 2*(ALPHABET_SIZE-positionInPack-1));
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// Increment the packed counter. If all possible bases have been squeezed into this byte, write it out.
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positionInPack = ++positionInPack % ALPHABET_SIZE;
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if( positionInPack == 0 ) {
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targetOutputStream.write(packedBases);
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packedBases = 0;
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}
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}
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/**
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* Writes an array of bases to the target output stream.
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* @param bases List of bases to write.
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* @throws IOException if an I/O error occurs.
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*/
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public void write( byte[] bases ) throws IOException {
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for(byte base: bases) write(base);
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}
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/**
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* Flush the contents of the OutputStream to disk.
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* @throws IOException if an I/O error occurs.
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*/
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public void flush() throws IOException {
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targetOutputStream.flush();
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}
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/**
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* Closes the given output stream.
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* @throws IOException if an I/O error occurs.
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*/
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public void close() throws IOException {
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// Write (incomplete) block in file, and number of bases in that last byte.
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if( positionInPack > 0 ) {
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targetOutputStream.write(packedBases);
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targetOutputStream.write(positionInPack);
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}
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else
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targetOutputStream.write(ALPHABET_SIZE);
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targetOutputStream.close();
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}
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/**
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* Gets the two-bit representation of a base. A=00b, C=01b, G=10b, T=11b.
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* @param base ASCII value for the base to pack.
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* @return A byte from 0-3 indicating the base's packed value.
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*/
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public static byte getPackedRepresentation(byte base) {
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switch( base ) {
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case 'A':
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return 0;
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case 'C':
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return 1;
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case 'G':
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return 2;
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case 'T':
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return 3;
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default:
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throw new StingException("Unknown base type: " + base);
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}
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}
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}
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