/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 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.broad.igv.bbfile;
import htsjdk.samtools.seekablestream.SeekableStream;
import org.apache.log4j.Logger;
import org.broad.igv.util.CompressionUtils;
import org.broad.igv.util.LittleEndianInputStream;
import java.io.ByteArrayOutputStream;
import java.util.ArrayList;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.DataInputStream;
import java.util.HashMap;
/**
* Created by IntelliJ IDEA.
* User: martind
* Date: Jan 26, 2010
* Time: 12:18:32 PM
* To change this template use File | Settings | File Templates.
*/
/*
* Container class for reading and storing a block of bed data items.
* */
public class BigBedDataBlock {
private static Logger log = Logger.getLogger(BigBedDataBlock.class);
// Bed data block access variables - for reading in bed records from a file
private long fileOffset; // Bed data block file offset
private long dataBlockSize; // byte size for data block specified in the R+ leaf
private boolean isLowToHigh; // if true, data is low to high byte order; else high to low
// defines the bigBed/bigWig source chromosomes
private HashMap<Integer, String> chromosomeMap; // map of chromosome ID's and corresponding names
private RPTreeLeafNodeItem leafHitItem; // R+ tree leaf item containing data block location
// Provides uncompressed byte stream data reader
private byte[] bedBuffer; // buffer containing leaf block data uncompressed
private int remDataSize; // number of unread data bytes
// byte stream readers
private LittleEndianInputStream lbdis; // low to high byte stream reader
private DataInputStream dis; // high to low byte stream reader
// Bed data extraction members
private ArrayList<BedFeature> bedFeatureList; // array of BigBed data
/*
* Constructor for Bed data block reader.
*
* Parameters:
* fis - file input stream handle
* leafItem - R+ tree leaf item containing chromosome region and file data location
* chromIDTree - B+ chromosome index tree returns chromosome ID's for names
* isLowToHigh - byte order is low to high if true; else high to low
* uncompressBufSize - byte size for decompression buffer; else 0 for uncompressed
* */
public BigBedDataBlock(SeekableStream fis, RPTreeLeafNodeItem leafHitItem,
HashMap<Integer, String> chromosomeMap, boolean isLowToHigh, int uncompressBufSize) {
this.leafHitItem = leafHitItem;
this.chromosomeMap = chromosomeMap;
this.isLowToHigh = isLowToHigh;
dataBlockSize = this.leafHitItem.geDataSize();
byte[] buffer = new byte[(int) dataBlockSize];
fileOffset = this.leafHitItem.getDataOffset();
// read Bed data block into a buffer
try {
fis.seek(fileOffset);
fis.readFully(buffer);
// decompress if necessary - the buffer size is 0 for uncompressed data
// Note: BBFile Table C specifies a decompression buffer size
if (uncompressBufSize > 0)
bedBuffer = (new CompressionUtils()).decompress(buffer, uncompressBufSize);
else
bedBuffer = buffer; // use uncompressed read buffer directly
} catch (IOException ex) {
String error = String.format("Error reading Bed data for leaf item %d \n");
log.error(error, ex);
throw new RuntimeException(error, ex);
}
// wrap the bed buffer as an input stream
if (this.isLowToHigh)
lbdis = new LittleEndianInputStream(new ByteArrayInputStream(bedBuffer));
else
dis = new DataInputStream(new ByteArrayInputStream(bedBuffer));
// initialize unread data size
remDataSize = bedBuffer.length;
// use methods getBedData or getNextFeature to extract block data
}
/*
* Method returns all Bed features within the decompressed block buffer
*
* Parameters:
* selectionRegion - chromosome region for selecting Bed features
* contained - indicates selected data must be contained in selection region
* if true, else may intersect selection region
*
* Returns:
* Bed feature items in the data block
*
* Note: Remaining bytes to data block are used to determine end of reading
* since a zoom record count for the data block is not known.
* */
public ArrayList<BedFeature> getBedData(RPChromosomeRegion selectionRegion,
boolean contained) {
int itemNumber = 0;
int chromID, chromStart, chromEnd;
String restOfFields;
// chromID + chromStart + chromEnd + rest 0 byte
// 0 byte for "restOfFields" is always present for bed data
int minItemSize = 3 * 4 + 1;
// allocate the bed feature array list
bedFeatureList = new ArrayList<BedFeature>();
try {
for (int index = 0; remDataSize >= minItemSize; ++index) {
itemNumber = index + 1;
// read in BigBed item fields - BBFile Table I
if (isLowToHigh) {
chromID = lbdis.readInt();
chromStart = lbdis.readInt();
chromEnd = lbdis.readInt();
restOfFields = lbdis.readString();
} else {
chromID = dis.readInt();
chromStart = dis.readInt();
chromEnd = dis.readInt();
restOfFields = readHighToLowString();
}
int leafHitValue = selectionRegion.compareRegions(chromID, chromStart, chromID, chromEnd);
if (leafHitValue == -2 || (contained && leafHitValue == -1)) {
remDataSize -= (minItemSize + restOfFields.length());
break;
}
if (leafHitValue == 2 || (contained && leafHitValue == 1)) {
remDataSize -= (minItemSize + restOfFields.length());
continue;
} else {
remDataSize -= (minItemSize + restOfFields.length());
String chromosome = chromosomeMap.get(chromID);
BedFeature bbItem = new BedFeature(itemNumber, chromosome, chromStart, chromEnd, restOfFields);
bedFeatureList.add(bbItem);
}
}
} catch (IOException ex) {
log.error("Read error for Bed data item " + itemNumber, ex);
// accept this as an end of block condition unless no items were read
if (itemNumber == 1)
throw new RuntimeException("Read error for Bed data item " + itemNumber, ex);
}
return bedFeatureList;
}
private String readHighToLowString() throws IOException {
String restOfFields;
ByteArrayOutputStream bis = new ByteArrayOutputStream(100);
byte b;
while ((b = (byte) dis.read()) != 0) {
bis.write(b);
}
restOfFields = new String(bis.toByteArray());
return restOfFields;
}
public void print() {
log.debug("BigBed data for " + bedFeatureList.size() + " items");
for (int index = 0; index <= bedFeatureList.size(); ++index) {
// BigBed data items print themselves
bedFeatureList.get(index).print();
}
}
}