-
Notifications
You must be signed in to change notification settings - Fork 387
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
11 changed files
with
160 additions
and
432 deletions.
There are no files selected for viewing
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
311 changes: 31 additions & 280 deletions
311
src/main/java/org/broad/igv/bbfile/BBFileHeader.java
100755 → 100644
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,288 +1,39 @@ | ||
| /* | ||
| * 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; | ||
|
|
||
| /** | ||
| * Created by IntelliJ IDEA. | ||
| * User: martind | ||
| * Date: Nov 20, 2009 | ||
| * Time: 3:49:14 PM | ||
| * To change this template use File | Settings | File Templates. | ||
| */ | ||
| import org.broad.igv.logging.LogManager; | ||
| import org.broad.igv.logging.Logger; | ||
| import org.broad.igv.util.ByteBufferUnsigned; | ||
|
|
||
| /** | ||
| * Container class defines the header information for BigBed and BigWig files | ||
| * BB File header -- supplemental table 5. Common header for BigWig and BigBed files. 64 bytes in size. | ||
| */ | ||
| package org.broad.igv.bbfile; | ||
|
|
||
|
|
||
| import htsjdk.samtools.seekablestream.SeekableStream; | ||
| import org.broad.igv.logging.*; | ||
| import org.broad.igv.util.LittleEndianInputStream; | ||
|
|
||
| import java.io.ByteArrayInputStream; | ||
| import java.io.DataInputStream; | ||
| import java.io.IOException; | ||
|
|
||
| /* | ||
| * Container class for holding the BBFile header information, Table C . | ||
| **/ | ||
| public class BBFileHeader { | ||
|
|
||
| private static Logger log = LogManager.getLogger(BBFileHeader.class); | ||
|
|
||
| // defines bigBed/bigwig Header Format types | ||
| static public final int BBFILE_HEADER_SIZE = 64; | ||
|
|
||
| static public final int BIGWIG_MAGIC_LTH = 0x888FFC26; // BigWig Magic Low to High | ||
| static public final int BIGWIG_MAGIC_HTL = 0x26FC8F66; // BigWig Magic High to Low | ||
|
|
||
| static public final int BIGBED_MAGIC_LTH = 0x8789F2EB; // BigBed Magic Low to High | ||
| static public final int BIGBED_MAGIC_HTL = 0xEBF28987; // BigBed Magic High to Low | ||
|
|
||
| // defines the bigBed/bigWig source file access | ||
| private String path; // bigBed file/pathname | ||
| private SeekableStream fis; // BBFile I/O stream handle | ||
| private long fileHeaderOffset; // file offset for file header | ||
|
|
||
| private boolean isHeaderOK; // File header read correctly? | ||
| private boolean isLowToHigh; // flag indicates values represented low to high bytes | ||
| private boolean isBigBed; // flag indicates file is BigBed format | ||
| private boolean isBigWig; // flag indicates file is BigWig format; | ||
|
|
||
| // BBFile Header items - Table C: | ||
| // mMagic number (4 bytes) indicates file type and byte order : | ||
| // 0x888FFC26 for bigWig, little endian if swapped | ||
| // 0x8789F2EB for bigBed, little endian if swapped | ||
| private int magic; // 4 byte mMagic Number | ||
| private int version; // 2 byte version ID; currently 3 | ||
| private int nZoomLevels; // 2 byte count of zoom sumary levels | ||
| private long chromTreeOffset; // 8 byte offset to mChromosome B+ Tree index | ||
| private long fullDataOffset; // 8 byte offset to unzoomed data dataCount | ||
| private long fullIndexOffset; // 8 byte offset to R+ Tree index of items | ||
| private int fieldCount; // 2 byte number of fields in bed. (0 for bigWig) | ||
| private int definedFieldCount; // 2 byte number of fields that are bed fields | ||
| private long autoSqlOffset; // 8 byte offset to 0 terminated string with .as spec | ||
| private long totalSummaryOffset; // 8 byte offset to file summary data block | ||
| private int uncompressBuffSize; // 4 byte maximum size for decompressed buffer | ||
| private long reserved; // 8 bytes reserved for future expansion. Currently 0 | ||
|
|
||
| // constructor reads BBFile header from an input stream | ||
| public BBFileHeader(String path, SeekableStream fis, long fileOffset) { | ||
|
|
||
| // save the path and seekable file handle | ||
| this.path = path; | ||
| this.fis = fis; | ||
| fileHeaderOffset = fileOffset; | ||
|
|
||
| // read in BBFile header | ||
| isHeaderOK = readBBFileHeader(fileHeaderOffset); | ||
| } | ||
|
|
||
|
|
||
| public String getPath() { | ||
| return path; | ||
| } | ||
|
|
||
| public boolean isHeaderOK() { | ||
| return isHeaderOK; | ||
| } | ||
|
|
||
| public boolean isLowToHigh() { | ||
| return isLowToHigh; | ||
| } | ||
|
|
||
| public boolean isBigBed() { | ||
| return isBigBed; | ||
| } | ||
|
|
||
| public boolean isBigWig() { | ||
| return isBigWig; | ||
| } | ||
|
|
||
| public int getFileHeaderSize() { | ||
| return BBFILE_HEADER_SIZE; | ||
| } | ||
|
|
||
| // ************* return header items **************** | ||
|
|
||
| public int getMagic() { | ||
| return magic; | ||
| } | ||
|
|
||
| public int getVersion() { | ||
| return version; | ||
| } | ||
|
|
||
| public int getZoomLevels() { | ||
| return nZoomLevels; | ||
| } | ||
|
|
||
| public long getChromosomeTreeOffset() { | ||
| return chromTreeOffset; | ||
| } | ||
|
|
||
| public long getFullDataOffset() { | ||
| return fullDataOffset; | ||
| } | ||
|
|
||
| public long getFullIndexOffset() { | ||
| return fullIndexOffset; | ||
| } | ||
|
|
||
| public int getFieldCount() { | ||
| return fieldCount; | ||
| } | ||
|
|
||
| public int getDefinedFieldCount() { | ||
| return definedFieldCount; | ||
| } | ||
|
|
||
| public long getAutoSqlOffset() { | ||
| return autoSqlOffset; | ||
| } | ||
|
|
||
| public long getTotalSummaryOffset() { | ||
| return totalSummaryOffset; | ||
| } | ||
|
|
||
| public int getUncompressBuffSize() { | ||
| return uncompressBuffSize; | ||
| } | ||
|
|
||
|
|
||
| public void print() { | ||
|
|
||
| if (isHeaderOK) { | ||
| if (isBigWig()) | ||
| System.out.println("BigWig file " + path + ", file header at location " + fileHeaderOffset); | ||
| else if (isBigBed()) | ||
| System.out.println("BigBed file " + path + ", file header at location " + fileHeaderOffset); | ||
| } else { | ||
| System.out.println("BBFile " + path + " with bad magic = " + magic + | ||
| " from file header location " + fileHeaderOffset); | ||
| return; // bad read - remaining header items not interpreted | ||
| } | ||
|
|
||
|
|
||
| // header fields | ||
| System.out.println("BBFile header magic = " + magic); | ||
| System.out.println("Version = " + version); | ||
| System.out.println("Zoom Levels = " + nZoomLevels); | ||
| System.out.println("Chromosome Info B+ tree offset = " + chromTreeOffset); | ||
| System.out.println("Data Block offset = " + fullDataOffset); | ||
| System.out.println("Chromosome Data R+ tree offset = " + fullIndexOffset); | ||
| System.out.println("Bed fields count = " + fieldCount); | ||
| System.out.println("Bed defined fields count = " + definedFieldCount); | ||
| System.out.println("AutoSql Offset = " + autoSqlOffset); | ||
| System.out.println("Total Summary offset = " + totalSummaryOffset); | ||
| System.out.println("Maximum uncompressed buffer size = " + uncompressBuffSize); | ||
| System.out.println("m_reserved = " + reserved); | ||
| } | ||
|
|
||
| /* | ||
| * Reads in BBFile header information. | ||
| * | ||
| * Returns: | ||
| * Success status flag is true for successfully read header, | ||
| * or is false for a read error. | ||
| **/ | ||
| private boolean readBBFileHeader(long fileOffset) { | ||
|
|
||
| BBFileHeader bbHeader = null; | ||
| LittleEndianInputStream lbdis = null; | ||
| DataInputStream bdis = null; | ||
|
|
||
| byte[] buffer = new byte[BBFILE_HEADER_SIZE]; | ||
|
|
||
|
|
||
| try { | ||
| // Read bigBed header into a buffer | ||
| fis.seek(fileOffset); | ||
| fis.readFully(buffer); | ||
|
|
||
| // decode header - determine byte order from first 4 bytes | ||
| // first assume byte order is low to high | ||
| isLowToHigh = true; | ||
| lbdis = new LittleEndianInputStream(new ByteArrayInputStream(buffer)); | ||
| magic = lbdis.readInt(); | ||
|
|
||
| // check for a valid bigBed or bigWig file | ||
| if (magic == BIGWIG_MAGIC_LTH) { | ||
| isBigWig = true; | ||
| } else if (magic == BIGBED_MAGIC_LTH) { | ||
| isBigBed = true; | ||
| } else { | ||
| bdis = new DataInputStream(new ByteArrayInputStream(buffer)); | ||
| magic = bdis.readInt(); | ||
|
|
||
| // check for a valid bigBed or bigWig file | ||
| if (magic == BIGWIG_MAGIC_HTL) | ||
| isBigWig = true; | ||
| else if (magic == BIGBED_MAGIC_HTL) | ||
| isBigBed = true; | ||
|
|
||
| else | ||
| return false; // can't identify BBFile type | ||
|
|
||
| // success - set order high to low | ||
| isLowToHigh = false; | ||
| } | ||
|
|
||
| // Get header information | ||
| if (isLowToHigh) { | ||
| version = lbdis.readUShort(); | ||
| nZoomLevels = lbdis.readUShort(); | ||
| chromTreeOffset = lbdis.readLong(); | ||
| fullDataOffset = lbdis.readLong(); | ||
| fullIndexOffset = lbdis.readLong(); | ||
| fieldCount = lbdis.readUShort(); | ||
| definedFieldCount = lbdis.readUShort(); | ||
| autoSqlOffset = lbdis.readLong(); | ||
| totalSummaryOffset = lbdis.readLong(); | ||
| uncompressBuffSize = lbdis.readInt(); | ||
| reserved = lbdis.readLong(); | ||
| } else { | ||
| version = (short) bdis.readUnsignedShort(); | ||
| nZoomLevels = (short) bdis.readUnsignedShort(); | ||
| chromTreeOffset = bdis.readLong(); | ||
| fullDataOffset = bdis.readLong(); | ||
| fullIndexOffset = bdis.readLong(); | ||
| fieldCount = (short) bdis.readUnsignedShort(); | ||
| definedFieldCount = (short) bdis.readUnsignedShort(); | ||
| autoSqlOffset = bdis.readLong(); | ||
| totalSummaryOffset = bdis.readLong(); | ||
| uncompressBuffSize = bdis.readInt(); | ||
| reserved = bdis.readLong(); | ||
| } | ||
|
|
||
| } catch (IOException ex) { | ||
| throw new RuntimeException("Error reading file header for " + path, ex); | ||
| } | ||
|
|
||
| // file header was read properly | ||
| return true; | ||
| } | ||
|
|
||
| } // mEndBase of class BBFileHeader | ||
| int version; // 2 byte version ID; currently 3 | ||
| int nZoomLevels; // 2 byte count of zoom sumary levels | ||
| long chromTreeOffset; // 8 byte offset to mChromosome B+ Tree index | ||
| long fullDataOffset; // 8 byte offset to unzoomed data dataCount | ||
| long fullIndexOffset; // 8 byte offset to R+ Tree index of items | ||
| int fieldCount; // 2 byte number of fields in bed. (0 for bigWig) | ||
| int definedFieldCount; // 2 byte number of fields that are bed fields | ||
| long autoSqlOffset; // 8 byte offset to 0 terminated string with .as spec | ||
| long totalSummaryOffset; // 8 byte offset to file summary data block | ||
| int uncompressBuffSize; | ||
| long extensionOffset; | ||
|
|
||
| public BBFileHeader(ByteBufferUnsigned bb) { | ||
| this.version = bb.getUShort(); | ||
| this.nZoomLevels = bb.getUShort(); | ||
| this.chromTreeOffset = bb.getLong(); | ||
| this.fullDataOffset = bb.getLong(); | ||
| this.fullIndexOffset = bb.getLong(); | ||
| this.fieldCount = bb.getUShort(); | ||
| this.definedFieldCount = bb.getUShort(); | ||
| this.autoSqlOffset = bb.getLong(); | ||
| this.totalSummaryOffset = bb.getLong(); | ||
| this.uncompressBuffSize = bb.getInt(); | ||
| this.extensionOffset = bb.getLong(); | ||
| } | ||
| } |
Oops, something went wrong.