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Cleanup. Separate common packing functionality into utils class. Make base packing utility as generic as possible. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1566 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-09-09 17:54:12 +00:00
parent 3b1e966b4c
commit 43d1c6741c
7 changed files with 214 additions and 296 deletions
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120
java/src/org/broadinstitute/sting/bwa/BasePackedOutputStream.java 100644
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@ -0,0 +1,120 @@
package org.broadinstitute.sting.bwa;
import org.broadinstitute.sting.utils.StingException;
import java.io.*;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
/**
* A general-purpose stream for writing packed bases.
*
* @author mhanna
* @version 0.1
*/
public class BasePackedOutputStream<T> {
/**
* Type of object to pack.
*/
private final Class<T> type;
/**
* How many bases can be stored in the given data structure?
*/
private final int basesPerType;
/**
* Ultimate target for the packed bases.
*/
private final OutputStream targetOutputStream;
/**
* A fixed-size buffer for word-packed data.
*/
private final ByteBuffer buffer;
public BasePackedOutputStream( Class<T> type, File outputFile, ByteOrder byteOrder ) throws FileNotFoundException {
this(type,new BufferedOutputStream(new FileOutputStream(outputFile)),byteOrder);
}
/**
* Write packed bases to the given output stream.
* @param type Type of data to pack bases into.
* @param outputStream Output stream to which to write packed bases.
* @param byteOrder Switch between big endian / little endian when reading / writing files.
*/
public BasePackedOutputStream( Class<T> type, OutputStream outputStream, ByteOrder byteOrder) {
this.targetOutputStream = outputStream;
this.type = type;
basesPerType = PackUtils.bitsInType(type)/PackUtils.BITS_PER_BASE;
this.buffer = ByteBuffer.allocate(basesPerType/PackUtils.ALPHABET_SIZE).order(byteOrder);
}
/**
* Writes an array of bases to the target output stream.
* @param bases List of bases to write.
* @throws IOException if an I/O error occurs.
*/
public void write( byte[] bases ) throws IOException {
int packedBases = 0;
int positionInPack = 0;
for(byte base: bases) {
packedBases = packBase(base, packedBases, positionInPack);
// Increment the packed counter. If all possible bases have been squeezed into this byte, write it out.
positionInPack = ++positionInPack % basesPerType;
if( positionInPack == 0 ) {
writePackedBases(packedBases);
packedBases = 0;
}
}
if( positionInPack > 0 )
writePackedBases(packedBases);
}
/**
* Flush the contents of the OutputStream to disk.
* @throws IOException if an I/O error occurs.
*/
public void flush() throws IOException {
targetOutputStream.flush();
}
/**
* Closes the given output stream.
* @throws IOException if an I/O error occurs.
*/
public void close() throws IOException {
targetOutputStream.close();
}
/**
* Pack the given base into the basepack.
* @param base The base to pack.
* @param basePack Target for the pack operation.
* @param position Position within the pack to which to add the base.
* @return The packed integer.
*/
private int packBase( byte base, int basePack, int position ) {
basePack |= (PackUtils.packBase(base) << 2*(basesPerType-position-1));
return basePack;
}
/**
* Write the given packed base structure to the output file.
* @param packedBases Packed bases to write.
* @throws IOException on error writing to the file.
*/
private void writePackedBases(int packedBases) throws IOException {
buffer.rewind();
if( type == Integer.class )
buffer.putInt(packedBases);
else if( type == Byte.class )
buffer.put((byte)packedBases);
else
throw new StingException("Cannot pack bases into type " + type.getName());
targetOutputStream.write(buffer.array());
}
}

157
java/src/org/broadinstitute/sting/bwa/BytePackedOutputStream.java
View File

@ -1,157 +0,0 @@
/*
* Copyright (c) 2009 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.sting.bwa;
import org.broadinstitute.sting.utils.StingException;
import java.io.*;
/**
* Write packed bases to an output stream. Pack each base into 2 bits.
*
* @author mhanna
* @version 0.1
*/
public class BytePackedOutputStream {
/**
* How many possible bases can be encoded?
*/
public static final int ALPHABET_SIZE = 4;
/**
* Ultimate target for the packed bases.
*/
private final OutputStream targetOutputStream;
/**
* The next byte to write to the output stream. Will be added
* to the output stream when enough bases are accumulated, or when
* the file is closed.
*/
private byte packedBases;
/**
* Where will the next base be embedded into packedBases?
*/
private int positionInPack = 0;
public BytePackedOutputStream( File outputFile ) throws FileNotFoundException {
this(new BufferedOutputStream(new FileOutputStream(outputFile)));
}
/**
* Write packed bases to the given output stream.
* @param outputStream Output stream to which to write packed bases.
*/
public BytePackedOutputStream( OutputStream outputStream ) {
this.targetOutputStream = outputStream;
}
/**
* Write a given base to the output stream.
* @param base Base to write.
* @throws IOException if an I/O error occurs.
*/
public void write( byte base ) throws IOException {
packedBases |= (getPackedRepresentation(base) << 2*(ALPHABET_SIZE-positionInPack-1));
// Increment the packed counter. If all possible bases have been squeezed into this byte, write it out.
positionInPack = ++positionInPack % ALPHABET_SIZE;
if( positionInPack == 0 ) {
targetOutputStream.write(packedBases);
packedBases = 0;
}
}
/**
* Writes an array of bases to the target output stream.
* @param bases List of bases to write.
* @throws IOException if an I/O error occurs.
*/
public void write( byte[] bases ) throws IOException {
for(byte base: bases) write(base);
}
/**
* Flush the contents of the OutputStream to disk.
* @throws IOException if an I/O error occurs.
*/
public void flush() throws IOException {
targetOutputStream.flush();
}
/**
* Closes the given output stream.
* @throws IOException if an I/O error occurs.
*/
public void close() throws IOException {
// Write (incomplete) block in file, and number of bases in that last byte.
if( positionInPack > 0 ) {
targetOutputStream.write(packedBases);
targetOutputStream.write(positionInPack);
}
else
targetOutputStream.write(ALPHABET_SIZE);
targetOutputStream.close();
}
/**
* Gets the two-bit representation of a base. A=00b, C=01b, G=10b, T=11b.
* @param base ASCII value for the base to pack.
* @return A byte from 0-3 indicating the base's packed value.
*/
public static byte getPackedRepresentation(byte base) {
switch( base ) {
case 'A':
return 0;
case 'C':
return 1;
case 'G':
return 2;
case 'T':
return 3;
default:
throw new StingException("Unknown base type: " + base);
}
}
public static byte decodePackedRepresentation(byte pack) {
switch( pack ) {
case 0:
return 'A';
case 1:
return 'C';
case 2:
return 'G';
case 3:
return 'T';
default:
throw new StingException("Unknown pack type: " + pack);
}
}
}

5
java/src/org/broadinstitute/sting/bwa/CreateBWTFromReference.java
View File

@ -33,7 +33,6 @@ import net.sf.samtools.util.StringUtil;
import java.io.*;
import java.util.TreeSet;
import java.util.Comparator;
import java.util.Arrays;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
@ -56,7 +55,7 @@ public class CreateBWTFromReference {
private int[] countOccurrences( String sequence ) {
int occurrences[] = new int[ALPHABET_SIZE];
for( char base: sequence.toCharArray() )
occurrences[ BytePackedOutputStream.getPackedRepresentation((byte)base) ]++;
occurrences[PackUtils.packBase((byte)base)]++;
// Make occurrences cumulative
for( int i = 1; i < ALPHABET_SIZE; i++ )
@ -182,7 +181,7 @@ public class CreateBWTFromReference {
occurrenceWriter.write(occurrences);
occurrenceWriter.flush();
WordPackedOutputStream sequenceOutputStream = new WordPackedOutputStream(bwtOutputStream,ByteOrder.LITTLE_ENDIAN);
BasePackedOutputStream<Integer> sequenceOutputStream = new BasePackedOutputStream<Integer>(Integer.class,bwtOutputStream,ByteOrder.LITTLE_ENDIAN);
sequenceOutputStream.write(bwt);
sequenceOutputStream.close();

9
java/src/org/broadinstitute/sting/bwa/CreatePACFromReference.java
View File

@ -30,6 +30,7 @@ import net.sf.picard.reference.ReferenceSequenceFileFactory;
import net.sf.picard.reference.ReferenceSequence;
import java.io.*;
import java.nio.ByteOrder;
/**
* Generate a .PAC file from a given reference.
@ -53,9 +54,13 @@ public class CreatePACFromReference {
// Target file for output
File outputFile = new File(argv[1]);
BytePackedOutputStream outputStream = new BytePackedOutputStream(outputFile);
OutputStream outputStream = new FileOutputStream(outputFile);
BasePackedOutputStream<Byte> basePackedOutputStream = new BasePackedOutputStream<Byte>(Byte.class, outputStream, ByteOrder.BIG_ENDIAN);
basePackedOutputStream.write(sequence.getBases());
outputStream.write(sequence.getBases().length%PackUtils.ALPHABET_SIZE);
outputStream.write(sequence.getBases());
outputStream.close();
}
}

82
java/src/org/broadinstitute/sting/bwa/PackUtils.java 100644
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@ -0,0 +1,82 @@
package org.broadinstitute.sting.bwa;
import org.broadinstitute.sting.utils.StingException;
/**
* Utilities designed for packing / unpacking bases.
*
* @author mhanna
* @version 0.1
*/
public class PackUtils {
/**
* How many possible bases can be encoded?
*/
public static final int ALPHABET_SIZE = 4;
/**
* How many bits does it take to store a single base?
*/
public static final int BITS_PER_BASE = (int)(Math.log(ALPHABET_SIZE)/Math.log(2));
/**
* How many bits fit into a single byte?
*/
public static final int BITS_PER_BYTE = 8;
/**
* How many bits can a given type hold?
* @param type Type to test.
* @return Number of bits that the given type can hold.
*/
public static final int bitsInType( Class<?> type ) {
try {
long typeSize = type.getField("MAX_VALUE").getLong(null) - type.getField("MIN_VALUE").getLong(null)+1;
long intTypeSize = (long)Integer.MAX_VALUE - (long)Integer.MIN_VALUE + 1;
if( typeSize > intTypeSize )
throw new StingException("Cannot determine number of bits available in type: " + type.getName());
return (int)(Math.log(typeSize)/Math.log(2));
}
catch( NoSuchFieldException ex ) {
throw new StingException("Cannot determine number of bits available in type: " + type.getName(),ex);
}
catch( IllegalAccessException ex ) {
throw new StingException("Cannot determine number of bits available in type: " + type.getName(),ex);
}
}
/**
* Gets the two-bit representation of a base. A=00b, C=01b, G=10b, T=11b.
* @param base ASCII value for the base to pack.
* @return A byte from 0-3 indicating the base's packed value.
*/
public static byte packBase(byte base) {
switch( base ) {
case 'A':
return 0;
case 'C':
return 1;
case 'G':
return 2;
case 'T':
return 3;
default:
throw new StingException("Unknown base type: " + base);
}
}
public static byte unpackBase(byte pack) {
switch( pack ) {
case 0:
return 'A';
case 1:
return 'C';
case 2:
return 'G';
case 3:
return 'T';
default:
throw new StingException("Unknown pack type: " + pack);
}
}
}

6
java/src/org/broadinstitute/sting/bwa/WordPackedInputStream.java
View File

@ -26,7 +26,7 @@ public class WordPackedInputStream {
public WordPackedInputStream( File inputFile, ByteOrder byteOrder ) throws FileNotFoundException {
this.targetInputStream = new BufferedInputStream(new FileInputStream(inputFile));
this.buffer = ByteBuffer.allocate(WordPackedOutputStream.BASES_PER_WORD/BytePackedOutputStream.ALPHABET_SIZE).order(byteOrder);
this.buffer = ByteBuffer.allocate(PackUtils.bitsInType(Integer.class)/PackUtils.BITS_PER_BYTE).order(byteOrder);
}
/**
@ -44,9 +44,9 @@ public class WordPackedInputStream {
List<Byte> bwtList = new ArrayList<Byte>();
while(targetInputStream.read(buffer.array()) > 0) {
int packedWord = buffer.getInt();
for( int i = WordPackedOutputStream.BASES_PER_WORD-1; i >= 0; i-- ) {
for( int i = PackUtils.bitsInType(Integer.class)/PackUtils.BITS_PER_BASE - 1; i >= 0; i-- ) {
byte packedByte = (byte)((packedWord >> i*2) & 0x3);
bwtList.add(BytePackedOutputStream.decodePackedRepresentation(packedByte));
bwtList.add(PackUtils.unpackBase(packedByte));
}
buffer.rewind();
}

131
java/src/org/broadinstitute/sting/bwa/WordPackedOutputStream.java
View File

@ -1,131 +0,0 @@
/*
* Copyright (c) 2009 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.sting.bwa;
import java.io.*;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
/**
* Word-pack bases into the output stream. Bytes are stored as
* little-endian unsigned ints.
*
* @author mhanna
* @version 0.1
*/
public class WordPackedOutputStream {
/**
* How many bases can be stored in the given word?
*/
public static final int BASES_PER_WORD = 16;
/**
* Ultimate target for the packed bases.
*/
private final OutputStream targetOutputStream;
/**
* The next byte to write to the output stream. Will be added
* to the output stream when enough bases are accumulated, or when
* the file is closed.
*/
private int packedBases;
/**
* Where will the next base be embedded into packedBases?
*/
private int positionInPack = 0;
/**
* A fixed-size buffer for word-packed data.
*/
private final ByteBuffer buffer;
public WordPackedOutputStream( File outputFile, ByteOrder byteOrder ) throws FileNotFoundException {
this(new BufferedOutputStream(new FileOutputStream(outputFile)),byteOrder);
}
/**
* Write packed bases to the given output stream.
* @param outputStream Output stream to which to write packed bases.
* @param byteOrder Switch between big endian / little endian when reading / writing files.
*/
public WordPackedOutputStream(OutputStream outputStream, ByteOrder byteOrder) {
this.targetOutputStream = outputStream;
this.buffer = ByteBuffer.allocate(BASES_PER_WORD/BytePackedOutputStream.ALPHABET_SIZE).order(byteOrder);
}
/**
* Write a given base to the output stream.
* @param base Base to write.
* @throws IOException if an I/O error occurs.
*/
public void write( byte base ) throws IOException {
packedBases |= (BytePackedOutputStream.getPackedRepresentation(base) << 2*(BASES_PER_WORD-positionInPack-1));
// Increment the packed counter. If all possible bases have been squeezed into this byte, write it out.
positionInPack = ++positionInPack % BASES_PER_WORD;
if( positionInPack == 0 ) {
buffer.rewind();
buffer.putInt(packedBases);
targetOutputStream.write(buffer.array());
packedBases = 0;
}
}
/**
* Writes an array of bases to the target output stream.
* @param bases List of bases to write.
* @throws IOException if an I/O error occurs.
*/
public void write( byte[] bases ) throws IOException {
for(byte base: bases) write(base);
}
/**
* Flush the contents of the OutputStream to disk.
* @throws IOException if an I/O error occurs.
*/
public void flush() throws IOException {
targetOutputStream.flush();
}
/**
* Closes the given output stream.
* @throws IOException if an I/O error occurs.
*/
public void close() throws IOException {
// Write (incomplete) block in file, and number of bases in that last byte.
if( positionInPack > 0 ) {
buffer.rewind();
buffer.putInt(packedBases);
targetOutputStream.write(buffer.array());
}
targetOutputStream.close();
}
}