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/*
* Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
* WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
* WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
* PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
* OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
* TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
* OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
* ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
* THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
* SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*/
/** +-
* Created by IntelliJ IDEA.
* User: martind
* Date: Nov 20, 2009
* Time: 3:43:04 PM
* To change this template use File | Settings | File Templates.
*/
package org.broad.igv.bbfile;
import org.broad.tribble.util.LittleEndianInputStream;
import org.apache.log4j.Logger;
import org.broad.tribble.util.SeekableStream;
import org.broad.tribble.util.SeekableFileStream;
import java.io.*;
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);
// Defines the Big Binary File (BBFile) access
private String path; // BBFile source file/pathname
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 int dataCount; // Number of data records in the file - Table BB
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 long autoSqlOffset;
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 long mTotalSummaryBlockOffset;
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
public BBFileReader(String path) throws IOException {
this(path, new SeekableFileStream(new File(path)));
}
public BBFileReader(String path, SeekableStream stream) {
log.debug("Opening BBFile source " + path);
this.path = path;
fis = stream;
// 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
autoSqlOffset = fileHeader.getAutoSqlOffset();
if (autoSqlOffset != 0) {
// read in .as entry
// mFileOffset = mAutoSqlOffset + sizeof(.as format field);
}
// 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();
dataCount = getDataCount(fis, fileOffset);
}
/*
* Method returns the Big Binary File pathname.
*
* Returns:
* Big Binary File pathname
* */
public String getBBFilePath() {
return path;
}
/*
* Method returns the Big Binary File input stream handle.
*
* Returns:
* Big Binary File input stream handle
* */
public SeekableStream getBBFis() {
return fis;
}
/*
* 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 the total number of data records in the file.
*
* Returns:
* Count of the total number of compressed/uncompressed data records:
* which for BigBed is the number of bed features,
* and for BiGWifg is the number of wig sections.
* */
public int getDataCount() {
return dataCount;
}
/*
* Method returns the number of chromosomes/contigs in the file.
*
* Note: This is itemCount from B+ tree header BBFile Table E.
*
* Returns:
* Count of the total number of chromosomes/contigs in the file.
* */
public long getChromosomeNameCount() {
return chromosomeIDTree.getItemCount();
}
/*
* Method returns the number of chromosome/contig regions in the file.
*
* Note: This is itemCount from R+ tree header BBFile Table K.
*
* Returns:
* Count of the total number of chromosome/contig regions in the file.
* */
public long getChromosomeRegionCount() {
return chromosomeDataTree.getItemCount();
}
/*
* Method returns the Big Binary File decompressed buffer size.
*
* Returns:
* Largest required buffer size for decompressed data chunks (from Table C)
* */
public int getDecompressionBufSize() {
return uncompressBufSize;
}
/*
* 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 B+ Chromosome Index Tree.
*
* Returns:
* B+ Chromosome Index Tree (includes Tables E, F, G, H)
* */
public BPTree getChromosomeIDTree() {
return chromosomeIDTree;
}
/*
* Method returns the R+ Chromosome Data Locations Tree.
*
* Returns:
* R+ Chromosome Data Locations Tree (includes Tables K, L, M, N)
* */
public RPTree getChromosomeDataTree() {
return chromosomeDataTree;
}
/*
* Method returns number of zoom level data is included in the file.
*
* Returns:
* Number of zoom levels (from Table C)
* */
public int getZoomLevelCount() {
return zoomLevelCount;
}
/*
* 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 the zoom data bounds in R+ tree for a chromosome ID range.
*
* Parameters:
* zoomLevel - zoom level
* startChromID - start chromosome for the region
* endChromID - end chromosome for the region
*
* Returns:
* Chromosome region bounds for chromosome ID range
* */
public RPChromosomeRegion getZoomLevelBounds(int zoomLevel, int startChromID,
int endChromID) {
RPChromosomeRegion chromosomeBounds =
zoomLevels.getZoomLevelRPTree(zoomLevel).getChromosomeRegion(startChromID, endChromID);
return chromosomeBounds;
}
/*
* Method finds chromosome bounds for entire chromosome ID range in the zoom level R+ tree.
*
* Parameters:
* zoomLevel - zoom level
*
* Returns:
* Chromosome bounds for the entire chromosome ID range in the R+ tree.
* */
public RPChromosomeRegion getZoomLevelBounds(int zoomLevel) {
RPChromosomeRegion chromosomeBounds =
zoomLevels.getZoomLevelRPTree(zoomLevel).getChromosomeBounds();
return chromosomeBounds;
}
/*
* Method returns the zoom record count for the zoom level.
*
* Parameters:
* zoomLevel - zoom level
*
* Returns:
* Chromosome bounds for the entire chromosome ID range in the R+ tree.
* */
public int getZoomLevelRecordCount(int zoomLevel) {
return zoomLevels.getZoomLevelFormats().get(zoomLevel - 1).getZoomRecordCount();
}
/*
* Method finds chromosome key name for the associated chromosome ID in the B+ tree.
*
* Returns:
* chromosome key name for associated chromosome ID.
* */
public String getChromosomeName(int chromID) {
String chromosomeName = chromosomeIDTree.getChromosomeName(chromID);
return chromosomeName;
}
/*
* Method finds chromosome names in the B+ chromosome index tree.
*
* Returns:
* LIst of all chromosome key names in the B+ tree.
* */
public ArrayList getChromosomeNames() {
ArrayList chromosomeList = chromosomeIDTree.getChromosomeNames();
return chromosomeList;
}
/*
* Returns a chromosome ID which can be used to search for a
* corresponding data section in the R+ tree for data.
*
Parameters:
* chromosomeKey - chromosome name of valid key size.
*
*
* Note: A chromosomeID of -1 means chromosome name not included in B+ tree.
*
* */
public int getChromosomeID(String chromosomeKey) {
int chromosomeID = chromosomeIDTree.getChromosomeID(chromosomeKey);
return chromosomeID;
}
/*
* Method finds the chromosome bounding region in R+ tree for a chromosome ID range.
*
* Parameters:
* startChromID - start chromosome for the region
* endChromID - end chromosome for the region
*
* Returns:
* Chromosome region bounds for chromosome ID range
* */
public RPChromosomeRegion getChromosomeBounds(int startChromID, int endChromID) {
RPChromosomeRegion chromosomeBounds =
chromosomeDataTree.getChromosomeRegion(startChromID, endChromID);
return chromosomeBounds;
}
/*
* Method finds the chromosome bounds for the entire chromosome ID range in the R+ tree.
*
* Returns:
* chromosome bounds for the entire chromosome ID range in the R+ tree.
* */
public RPChromosomeRegion getChromosomeBounds() {
RPChromosomeRegion chromosomeBounds = chromosomeDataTree.getChromosomeBounds();
return chromosomeBounds;
}
/*
* Method finds all chromosome data regions in the R+ tree.
*
* Returns:
* List of chromosome ID's and regions.
* */
public ArrayList getChromosomeRegions() {
ArrayList regionList = chromosomeDataTree.getAllChromosomeRegions();
return regionList;
}
/*
* Method finds all zoom level data regions in the R+ tree.
*
* Parameters:
* int zoomLevel - zoom level
* Returns:
* List of chromosome ID's and regions for the zoom level.
* */
public ArrayList getZoomLevelRegions(int zoomLevel) {
ArrayList regionList =
zoomLevels.getZoomLevelRPTree(zoomLevel).getAllChromosomeRegions();
return regionList;
}
/**
* Returns an iterator for BigBed features which occupy a chromosome selection region.
*
* Note: the BBFile type should be BigBed; else a null iterator is returned.
*
* 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
*
* 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)
*/
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 BigBed features for all chromosome regions.
*
* Note: the BBFile type should be BigBed; else a null iterator is returned.
*
* Returns:
* Iterator to provide BedFeature(s) for all chromosome regions.
* 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)
*/
public BigBedIterator getBigBedIterator() {
if (!isBigBedFile())
return null;
// get all region bounds
RPChromosomeRegion selectionRegion = chromosomeDataTree.getChromosomeBounds();
// compose an iterator
boolean contained = true; /// all regions are contained
BigBedIterator bedIterator = new BigBedIterator(fis, chromosomeIDTree, chromosomeDataTree,
selectionRegion, contained);
return bedIterator;
}
/**
* Returns an iterator for BigWig values which occupy the specified startChromosome region.
*
* Note: the BBFile type should be BigWig; else a null iterator is returned.
*
* 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
*
* 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)
*/
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 BigWig values for all chromosome regions.
*
* Note: the BBFile type should be BigWig; else a null iterator is returned.
*
* Returns:
* Iterator to provide BedFeature(s) for all chromosome regions.
* 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)
*/
public BigWigIterator getBigWigIterator() {
if (!isBigWigFile())
return null;
// get all regions bounds
RPChromosomeRegion selectionRegion = chromosomeDataTree.getChromosomeBounds();
// compose an iterator
boolean contained = true; // all regions are contained
BigWigIterator wigIterator = new BigWigIterator(fis, chromosomeIDTree, chromosomeDataTree,
selectionRegion, contained);
return wigIterator;
}
/**
* Returns an iterator for zoom level records for the chromosome selection region.
*
* Note: the BBFile can be BigBed or BigWig.
*
* 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
*
* 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
*/
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.
*
* Note: the BBFile can be BigBed or BigWig.
*
* Parameters:
* zoomLevel - zoom level for data extraction; levels start at 1
*
* 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
*/
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;
}
/**
* Returns an iterator for zoom level records for the chromosome selection region.
*
* Note: the BBFile can be BigBed or BigWig.
*
* Parameters:
* zoomLevel - zoom level for data extraction; levels start at 1
* selectionRegion - chromosome selection region consists of:
* startChromID - ID of starting chromosome
* startBase - staring base position for features
* endChromID - ID of endind 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
*
* 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
*/
public ZoomLevelIterator getZoomLevelIterator(int zoomLevel, RPChromosomeRegion selectionRegion,
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);
/// compose an iterator
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;
}
/*
* Method reads data count which heads the data section of the BBFile.
*
* Returns:
* Data count of the number of data records:
* number of Bed features for BigBed
* number of Wig sections for BigWig
* */
private int getDataCount(SeekableStream fis, long fileOffset) {
int dataCount;
LittleEndianInputStream lbdis = null;
DataInputStream bdis = null;
// Note: dataCount in BBFile is simply a 4 byte int
// positioned at fullDataOffset in Table C
byte[] buffer = new byte[4];
try {
// read dataCount into a buffer
fis.seek(fileOffset);
fis.readFully(buffer);
// decode data count with proper byte stream reader
// first assume byte order is low to high
if (isLowToHigh) {
lbdis = new LittleEndianInputStream(new ByteArrayInputStream(buffer));
dataCount = lbdis.readInt();
} else {
bdis = new DataInputStream(new ByteArrayInputStream(buffer));
dataCount = bdis.readInt();
}
} catch (IOException ex) {
throw new RuntimeException("Error reading data count for all data", ex);
}
// data count was read properly
return dataCount;
}
} // end of BBFileReader
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