/*
* 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.stream.IGVSeekableBufferedStream;
import org.broad.igv.util.stream.IGVSeekableStreamFactory;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
/*
* Broad Institute Interactive Genome Viewer Big Binary File (BBFile) Reader
* - File reader for UCSC BigWig and BigBed file types.
*
* Notes: Table entries refer to Jim Kent of UCSC's document description:
* "BigWig and BigBed: Enabling Browsing of Large Distributed Data Sets",
* November 2009.
*
* The overall binary file layout is defined in Table B of the document.
*
* BBFile Reader sequences through this binary file layout:
*
* 1) Reads in BBFile Header Table C and determine if file is a valid Big Bed or Big Wig
* binary file type.
*
* 2) Reads in Zoom Header Tables D if zoom data is present, as defined by zoomLevels
* in Table C, one for each zoom level.
*
* 3) Reads in the AutoSQL block Table B if present, as referenced by autoSqlOffset in Table C.
*
* 4) Reads in Total Summary Block Table DD if present, as referenced by
* TotalSummaryOffset in Table C.
*
* 5) Reads in B+ Tree Header Chromosome Index Header Table E, as referenced
* by chromosomeTreeOffset in Table C.
*
* 6)Reads in B+ Tree Nodes indexing mChromosome ID's for mChromosome regions;
* Table F for node type (leaf/child), Table G for leaf items,
* Table H for child node items.
*
* 7) Reads in R+ Tree Chromosome ID Index Header Table K.
*
* 8) Reads in R+ Tree Nodes indexing of data arranged by mChromosome ID's;
* Table L for node type (leaf or child), Table M for leaf items,
* Table N for child node items.
*
* 9) Verifies Data Count of data records, as referenced by fullDataOffset in Table C
*
* 10) References data count records of data size defined in Table M of R+ Tree index
* for all leaf items in the tree.
*
* 11) Reads in zoom level format Table O for each zoom level comprised of
* zoom record count followed by that many Table P zoom statistics records,
* followed by an R+ tree of zoom data locations indexed as in Tables L, M, and N.
*
* 12) Returns information on chromosome name keys and chromosome data regions.
*
* 13) Provides iterators using chromosome names and data regions to extract
* zoom data, Wig data, and Bed data.
*
* */
public class BBFileReader {
public static final long BBFILE_HEADER_OFFSET = 0;
private static Logger log = Logger.getLogger(BBFileReader.class);
private SeekableStream fis; // BBFile input stream handle
private long fileOffset; // file offset for next item to be read
private BBFileHeader fileHeader; // Big Binary file header
private boolean isLowToHigh; // BBFile binary data format: low to high or high to low
private int uncompressBufSize; // buffer byte size for data decompression; 0 for uncompressed
// AutoSQL String defines custom BigBed formats
private String autoSqlFormat;
// This section defines the zoom items if zoom data exists
private int zoomLevelCount; // number of zoom levels defined
private long zoomLevelOffset; // file offset to zoom level headers
private BBZoomLevels zoomLevels; // zoom level headers and data locations
// Total Summary Block - file statistical info
private BBTotalSummaryBlock totalSummaryBlock;
// B+ tree
private long chromIDTreeOffset; // file offset to mChromosome index B+ tree
private BPTree chromosomeIDTree; // Container for the mChromosome index B+ tree
// R+ tree
private long chromDataTreeOffset; // file offset to mChromosome data R+ tree
private RPTree chromosomeDataTree; // Container for the mChromosome data R+ tree
private String autoSql;
public BBFileReader(String path) throws IOException {
log.debug("Opening BBFile source " + path);
fis = new IGVSeekableBufferedStream(IGVSeekableStreamFactory.getInstance().getStreamFor(path), 128000);
// read in file header
fileOffset = BBFILE_HEADER_OFFSET;
fileHeader = new BBFileHeader(path, fis, fileOffset);
//fileHeader.print();
if (!fileHeader.isHeaderOK()) {
log.error("BBFile header is unrecognized type, header magic = " + fileHeader.getMagic());
throw new RuntimeException("Error reading BBFile header for: " + path);
}
// get data characteristics
isLowToHigh = fileHeader.isLowToHigh();
uncompressBufSize = fileHeader.getUncompressBuffSize();
// update file offset past BBFile header
fileOffset += BBFileHeader.BBFILE_HEADER_SIZE;
// get zoom level count from file header
zoomLevelCount = fileHeader.getZoomLevels();
// extract zoom level headers and zoom data records
// Note: zoom headers Table D immediately follow the BBFile Header
if (zoomLevelCount > 0) {
zoomLevelOffset = fileOffset;
zoomLevels = new BBZoomLevels(fis, zoomLevelOffset, zoomLevelCount, isLowToHigh, uncompressBufSize);
// end of zoom level headers - compare with next BBFile item location
fileOffset += zoomLevelCount * BBZoomLevelHeader.ZOOM_LEVEL_HEADER_SIZE;
}
// get the AutoSQL custom BigBed fields
long autoSqlOffset = fileHeader.getAutoSqlOffset();
if (autoSqlOffset != 0) {
fis.seek(autoSqlOffset);
autoSql = readNullTerminatedString(fis);
}
// get the Total Summary Block (Table DD)
fileOffset = fileHeader.getTotalSummaryOffset();
if (fileHeader.getVersion() >= 2 && fileOffset > 0) {
totalSummaryBlock = new BBTotalSummaryBlock(fis, fileOffset, isLowToHigh);
fileOffset += BBTotalSummaryBlock.TOTAL_SUMMARY_BLOCK_SIZE;
}
// get Chromosome Data B+ Tree (Table E, F, G, H) : should always exist
chromIDTreeOffset = fileHeader.getChromosomeTreeOffset();
if (chromIDTreeOffset != 0) {
fileOffset = chromIDTreeOffset;
chromosomeIDTree = new BPTree(fis, fileOffset, isLowToHigh);
}
// get R+ chromosome data location tree (Tables K, L, M, N)
chromDataTreeOffset = fileHeader.getFullIndexOffset();
if (chromDataTreeOffset != 0) {
fileOffset = chromDataTreeOffset;
boolean forceDescend = false;
chromosomeDataTree = new RPTree(fis, fileOffset, isLowToHigh, uncompressBufSize, forceDescend);
}
// get number of data records indexed by the R+ chromosome data location tree
fileOffset = fileHeader.getFullDataOffset();
}
public void close() {
try {
fis.close();
} catch (IOException e) {
log.error("Error closing bigwig stream", e);
}
}
/*
* Method returns the Big Binary File header which identifies
* the file type and content.
*
* Returns:
* Big Binary File header (Table C)
* */
public BBFileHeader getBBFileHeader() {
return fileHeader;
}
/*
* Method returns if the Big Binary File is BigBed.
*
* Returns:
* Boolean identifies if Big Binary File is BigBed
* (recognized from magic number in file header Table C)
* */
public boolean isBigBedFile() {
return fileHeader.isBigBed();
}
/*
* Method returns if the Big Binary File is BigWig
*
* Returns:
* Boolean identifies if Big Binary File is BigWig
* (recognized from magic number in file header Table C)
* */
public boolean isBigWigFile() {
return fileHeader.isBigWig();
}
/*
* Method returns if the Big Binary File is written with a low to high byte
* order for formatted data.
*
* Returns:
* Boolean identifies if Big Binary File is low to high byte order
* (recognized from magic number in file header Table C); else is
* high to low byte order if false.
* */
public boolean isLowToHigh() {
return isLowToHigh;
}
/*
* Method returns the total summary block for the Big Binary File.
*
* Returns:
* Total summary block data statistics for the whole file (Table DD)
* */
public BBTotalSummaryBlock getTotalSummaryBlock() {
return totalSummaryBlock;
}
/*
* Method returns the zoom levels in the Big Binary File.
*
* Returns:
* Zoom level object containing zoom level headers and R+ zoom data locations tree
* (includes Tables D, O)
* */
public BBZoomLevels getZoomLevels() {
return zoomLevels;
}
/*
* Method finds chromosome names in the B+ chromosome index tree.
*
* Returns:
* LIst of all chromosome key names in the B+ tree.
* */
public ArrayList<String> getChromosomeNames() {
ArrayList<String> chromosomeList = chromosomeIDTree.getChromosomeNames();
return chromosomeList;
}
public String getAutoSql() {
return autoSql;
}
/**
* Returns an iterator for BigBed features which occupy a chromosome selection region.
* <p/>
* Note: the BBFile type should be BigBed; else a null iterator is returned.
* <p/>
* Parameters:
* startChromosome - name of start chromosome
* startBase - starting base position for features
* endChromosome - name of end chromosome
* endBase - ending base position for feature
* contained - flag specifies bed features must be contained in the specified
* base region if true; else can intersect the region if false
* <p/>
* Returns:
* Iterator to provide BedFeature(s) for the requested chromosome region.
* Error conditions:
* 1) An empty iterator is returned if region has no data available
* 2) A null object is returned if the file is not BigBed.(see isBigBedFile method)
*/
synchronized public BigBedIterator getBigBedIterator(String startChromosome, int startBase,
String endChromosome, int endBase, boolean contained) {
if (!isBigBedFile())
return null;
// go from chromosome names to chromosome ID region
RPChromosomeRegion selectionRegion = getChromosomeBounds(startChromosome, startBase,
endChromosome, endBase);
// check for valid selection region
if (selectionRegion == null)
return new BigBedIterator(); // an empty iterator
// compose an iterator
BigBedIterator bedIterator = new BigBedIterator(fis, chromosomeIDTree, chromosomeDataTree,
selectionRegion, contained);
return bedIterator;
}
/**
* Returns an iterator for BigWig values which occupy the specified startChromosome region.
* <p/>
* Note: the BBFile type should be BigWig; else a null iterator is returned.
* <p/>
* Parameters:
* startChromosome - name of start chromosome
* startBase - starting base position for features
* endChromosome - name of end chromosome
* endBase - ending base position for feature
* contained - flag specifies bed features must be contained in the specified
* base region if true; else can intersect the region if false
* <p/>
* Returns:
* Iterator to provide BedFeature(s) for the requested chromosome region.
* Error conditions:
* 1) An empty iterator is returned if region has no data available
* 2) A null object is returned if the file is not BigWig.(see isBigWigFile method)
*/
synchronized public BigWigIterator getBigWigIterator(String startChromosome, int startBase,
String endChromosome, int endBase, boolean contained) {
if (!isBigWigFile())
return null;
// go from chromosome names to chromosome ID region
RPChromosomeRegion selectionRegion = getChromosomeBounds(startChromosome, startBase,
endChromosome, endBase);
// check for valid selection region, return empty iterator if null
if (selectionRegion == null)
return new BigWigIterator();
// compose an iterator
BigWigIterator wigIterator = new BigWigIterator(fis, chromosomeIDTree, chromosomeDataTree,
selectionRegion, contained);
return wigIterator;
}
/**
* Returns an iterator for zoom level records for the chromosome selection region.
* <p/>
* Note: the BBFile can be BigBed or BigWig.
* <p/>
* Parameters:
* zoomLevel - zoom level for data extraction; levels start at 1
* startChromosome - start chromosome name
* startBase - staring base position for features
* endChromosome - end chromosome name
* endBase - ending base position for feature
* contained - flag specifies bed features must be contained in the
* specified base region if true; else can intersect the region if false
* <p/>
* Returns:
* Iterator to provide BedFeature(s) for the requested chromosome region.
* Error conditions:
* 1) An empty iterator is returned if region has no data available
*/
synchronized public ZoomLevelIterator getZoomLevelIterator(int zoomLevel, String startChromosome, int startBase,
String endChromosome, int endBase, boolean contained) {
// check for valid zoom level
if (zoomLevel < 1 || zoomLevel > zoomLevelCount)
throw new RuntimeException("Error: ZoomLevelIterator zoom level is out of range\n");
// get the appropriate zoom level R+ zoom data index tree
RPTree zoomDataTree = zoomLevels.getZoomLevelRPTree(zoomLevel);
// go from chromosome names to chromosome ID region
RPChromosomeRegion selectionRegion = getChromosomeBounds(startChromosome, startBase,
endChromosome, endBase);
// check for valid selection region
if (selectionRegion == null) {
return ZoomLevelIterator.EmptyIterator.theInstance;
}
/// compose an iterator
ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree,
zoomDataTree, zoomLevel, selectionRegion, contained);
return zoomIterator;
}
/**
* Returns an iterator for zoom level records for all chromosome regions.
* <p/>
* Note: the BBFile can be BigBed or BigWig.
* <p/>
* Parameters:
* zoomLevel - zoom level for data extraction; levels start at 1
* <p/>
* Returns:
* Iterator to provide BedFeature(s) for the requested chromosome region.
* Error conditions:
* 1) An empty iterator is returned if region has no data available
*/
synchronized public ZoomLevelIterator getZoomLevelIterator(int zoomLevel) {
// check for valid zoom level
if (zoomLevel < 1 || zoomLevel > zoomLevelCount)
throw new RuntimeException("Error: ZoomLevelIterator zoom level is out of range\n");
// get the appropriate zoom level R+ zoom data index tree
RPTree zoomDataTree = zoomLevels.getZoomLevelRPTree(zoomLevel);
// get all regions bounds
RPChromosomeRegion selectionRegion = zoomDataTree.getChromosomeBounds();
// compose an iterator
boolean contained = true; //all regions are contained
ZoomLevelIterator zoomIterator = new ZoomLevelIterator(fis, chromosomeIDTree,
zoomDataTree, zoomLevel, selectionRegion, contained);
return zoomIterator;
}
/*
* Method generates a chromosome bounds region for the supplied chromosome region name.
*
* Note: No attempt is made to verify the region exists in the file data, nor
* which data is being examined.
*
* Parameters:
* startChromosome - name of start chromosome
* startBase - starting base position for region
* endChromosome - name of end chromosome
* endBase - ending base position for region
*
* Returns:
* Chromosome bounds of a named chromosome region for data extraction;
* or null for regions not found in the B+ chromosome index tree.
* */
private RPChromosomeRegion getChromosomeBounds(String startChromosome, int startBase,
String endChromosome, int endBase) {
// If the chromosome name length is > the key size we can't distinguish it
if (startChromosome.length() > chromosomeIDTree.getKeySize()) {
return null;
}
// find the chromosome ID's using the name to get a valid name key, then associated ID
String startChromKey = chromosomeIDTree.getChromosomeKey(startChromosome);
int startChromID = chromosomeIDTree.getChromosomeID(startChromKey);
if (startChromID < 0) // mChromosome not in data?
return null;
String endChromKey = chromosomeIDTree.getChromosomeKey(endChromosome);
int endChromID = chromosomeIDTree.getChromosomeID(endChromKey);
if (endChromID < 0) // mChromosome not in data?
return null;
// create the bounding mChromosome region
RPChromosomeRegion chromBounds = new RPChromosomeRegion(startChromID, startBase,
endChromID, endBase);
return chromBounds;
}
private static String readNullTerminatedString(InputStream fis) throws IOException {
ByteArrayOutputStream bos = new ByteArrayOutputStream(100);
byte b;
while ((b = (byte) fis.read()) != 0) {
bos.write(b);
}
return new String(bos.toByteArray());
}
} // end of BBFileReader