picard.illumina.parser.readers.BclIndexReader Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2014 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 picard.illumina.parser.readers;
import picard.PicardException;
import java.io.File;
import java.nio.ByteBuffer;
/**
* Annoyingly, there are two different files with extension .bci in NextSeq output. This reader handles
* the file that contains virtual file pointers into a .bcl.bgzf file. After the header, there is a 64-bit record
* per tile.
*/
public class BclIndexReader {
private static final int BCI_HEADER_SIZE = 8;
private static final int BCI_VERSION = 0;
private final BinaryFileIterator bciIterator;
private final int numTiles;
private final File bciFile;
private int nextRecordNumber = 0;
public BclIndexReader(final File bclFile) {
bciFile = new File(bclFile.getAbsolutePath() + ".bci");
bciIterator = MMapBackedIteratorFactory.getLongIterator(BCI_HEADER_SIZE, bciFile);
final ByteBuffer headerBytes = bciIterator.getHeaderBytes();
final int actualVersion = headerBytes.getInt();
if (actualVersion != BCI_VERSION) {
throw new PicardException(String.format("Unexpected version number %d in %s", actualVersion, bciFile.getAbsolutePath()));
}
numTiles = headerBytes.getInt();
}
public int getNumTiles() {
return numTiles;
}
public long get(final int recordNumber) {
if (recordNumber < nextRecordNumber) {
throw new IllegalArgumentException("Can only read forward");
}
if (recordNumber > nextRecordNumber) {
bciIterator.skipElements(recordNumber - nextRecordNumber);
nextRecordNumber = recordNumber;
}
++nextRecordNumber;
return bciIterator.getElement();
}
public File getBciFile() {
return bciFile;
}
}