/*
* 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.bwt;
import org.broadinstitute.gatk.engine.alignment.reference.packing.BasePackedInputStream;
import org.broadinstitute.gatk.engine.alignment.reference.packing.PackUtils;
import org.broadinstitute.gatk.engine.alignment.reference.packing.UnsignedIntPackedInputStream;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.nio.ByteOrder;
/**
* Reads a BWT from a given file.
*
* @author mhanna
* @version 0.1
*/
public class BWTReader {
/**
* Input stream from which to read BWT data.
*/
private FileInputStream inputStream;
/**
* Create a new BWT reader.
* @param inputFile File in which the BWT is stored.
*/
public BWTReader( File inputFile ) {
try {
this.inputStream = new FileInputStream(inputFile);
}
catch( FileNotFoundException ex ) {
throw new ReviewedGATKException("Unable to open input file", ex);
}
}
/**
* Read a BWT from the input stream.
* @return The BWT stored in the input stream.
*/
public BWT read() {
UnsignedIntPackedInputStream uintPackedInputStream = new UnsignedIntPackedInputStream(inputStream, ByteOrder.LITTLE_ENDIAN);
BasePackedInputStream basePackedInputStream = new BasePackedInputStream<Integer>(Integer.class, inputStream, ByteOrder.LITTLE_ENDIAN);
long inverseSA0;
long[] count;
SequenceBlock[] sequenceBlocks;
try {
inverseSA0 = uintPackedInputStream.read();
count = new long[PackUtils.ALPHABET_SIZE];
uintPackedInputStream.read(count);
long bwtSize = count[PackUtils.ALPHABET_SIZE-1];
sequenceBlocks = new SequenceBlock[PackUtils.numberOfPartitions(bwtSize,BWT.SEQUENCE_BLOCK_SIZE)];
for( int block = 0; block < sequenceBlocks.length; block++ ) {
int sequenceStart = block* BWT.SEQUENCE_BLOCK_SIZE;
int sequenceLength = (int)Math.min(BWT.SEQUENCE_BLOCK_SIZE,bwtSize-sequenceStart);
long[] occurrences = new long[PackUtils.ALPHABET_SIZE];
byte[] bwt = new byte[sequenceLength];
uintPackedInputStream.read(occurrences);
basePackedInputStream.read(bwt);
sequenceBlocks[block] = new SequenceBlock(sequenceStart,sequenceLength,new Counts(occurrences,false),bwt);
}
}
catch( IOException ex ) {
throw new ReviewedGATKException("Unable to read BWT from input stream.", ex);
}
return new BWT(inverseSA0, new Counts(count,true), sequenceBlocks);
}
/**
* Close the input stream.
*/
public void close() {
try {
inputStream.close();
}
catch( IOException ex ) {
throw new ReviewedGATKException("Unable to close input file", ex);
}
}
}