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Variant annotation and effect prediction package.
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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.
*/
package org.broad.igv.bbfile;
import org.apache.log4j.Logger;
import org.broad.tribble.util.LittleEndianInputStream;
import java.io.ByteArrayInputStream;
import java.io.DataInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
/**
* Created by IntelliJ IDEA.
* User: Owner
* Date: May 3, 2010
* Time: 12:32:17 AM
* To change this template use File | Settings | File Templates.
*/
public class BigWigSection {
private static Logger log = Logger.getLogger(BigWigSection.class);
private boolean isLowToHigh; // byte order is low to high if true; else high to low
private LittleEndianInputStream lbdis; // input stream reader for low to high byte ordered data
private DataInputStream dis; // input stream reader for high to low byte ordered data
private RPTreeLeafNodeItem leafHitItem; // leaf item defines chromosome region and file data location
private int sectionDataSize; // byte size of decompressed data for this section
private HashMap chromosomeMap; // map of chromosome ID's and corresponding names
private BigWigSectionHeader wigSectionHeader; // wig section header
/*
* Constructor for a BigWig data section which includes the section header
* and Wig data items.
*
* Parameters:
* sectionBuffer - buffer contains decompressed Wig section header + data
* sectionIndex - wig section index for leaf data block
* chromIDTree - B+ chromosome index tree returns chromosome names for ID's
* isLowToHigh - if true, data byte order is low to high ; else is high to low
* leafHitItem - contains leaf node information for testing against selection region
*
* */
public BigWigSection(byte[] sectionBuffer, HashMap chromosomeMap,
boolean isLowToHigh, RPTreeLeafNodeItem leafHitItem){
this.chromosomeMap = chromosomeMap;
this.isLowToHigh = isLowToHigh;
this.leafHitItem = leafHitItem;
// wrap the Wig section buffer as an input stream and get the section header
// Note: A RuntimeException is thrown if header is not read properly
if(this.isLowToHigh) {
lbdis = new LittleEndianInputStream(new ByteArrayInputStream(sectionBuffer));
wigSectionHeader = new BigWigSectionHeader(lbdis);
}
else {
dis = new DataInputStream(new ByteArrayInputStream(sectionBuffer));
wigSectionHeader = new BigWigSectionHeader(dis);
}
// check for valid Wig item type
if(wigSectionHeader.getItemType() == BigWigSectionHeader.WigItemType.Unknown){
throw new RuntimeException("Read error on wig section leaf index ");
}
// include header in data segment size accounting
sectionDataSize = wigSectionHeader.SECTION_HEADER_SIZE;
// use method getSectionData to extract section data
}
/*
* Method returns the if the Wig items defined in this section are valid.
*
* Note: Use BigWigSectionHeader to obtain more information on
* Wig section data specifications.
*
* Returns:
* Specifies if Wig section has a valid data item type.
* */
public boolean isValidSectionType(){
return wigSectionHeader.IsValidType();
}
/*
* Method returns the Wig Section Header
*
* Returns:
* Wig section header
* */
public int getItemCount() {
return wigSectionHeader.getItemCount();
}
/*
* Method returns the Wig Section Header
*
* Returns:
* Wig section header
* */
public BigWigSectionHeader getSectionHeader() {
return wigSectionHeader;
}
/*
* Method returns the number bytes of decompressed data in this section.
*
* Returns:
* Number of uncompressed bytes read for the Wig data section
* */
public int getSectionDataSize() {
return sectionDataSize;
}
/*
* Method reads Wig data items within the decompressed block buffer for the selection region.
*
* Parameters:
* selectionRegion - chromosome selection region for item extraction
* contained - indicates select region must be contained in value region
* if true, else may intersect selection region for extraction
*
* Returns:
* Size in bytes for the wig data section.
* Items read in the wig segment data block are added to the wig item list .
*
* Note: Unlike ZoomLevel and BigBed formats, the Wig Section data block header contains
* an item count used to determine the end of data read.
* */
public int getSectionData(RPChromosomeRegion selectionRegion, boolean contained,
ArrayList wigItemList) {
// get the section's data item specifications
// Note: A RuntimeException is thrown if wig section header is not read properly
int chromID = wigSectionHeader.getChromID();
String chromosome = chromosomeMap.get(chromID);
int itemCount = wigSectionHeader.getItemCount();
int chromStart = wigSectionHeader.getChromosomeStart();
int chromEnd = wigSectionHeader.getChromosomeEnd();
int itemStep = wigSectionHeader.getItemStep();
int itemSpan = wigSectionHeader.getItemSpan();
int itemIndex = 0;
int startBase = 0;
int endBase = 0;
float value = 0.0f;
// find Wig data type - BBFile Table J item type
BigWigSectionHeader.WigItemType itemType = wigSectionHeader.getItemType();
// check if all leaf items are selection hits
RPChromosomeRegion itemRegion = new RPChromosomeRegion(chromID, chromStart,
chromID, chromEnd);
int leafHitValue = itemRegion.compareRegions(selectionRegion);
// extract Wig data records
// Note: the buffer input stream is positioned past section header
try {
for(int index = 0; index < itemCount; ++index) {
++itemIndex;
if(isLowToHigh){
if(itemType == BigWigSectionHeader.WigItemType.FixedStep){
startBase = chromStart;
endBase = startBase + itemSpan;
value = lbdis.readFloat();
chromStart = startBase + itemStep;
sectionDataSize += BigWigSectionHeader.FIXEDSTEP_ITEM_SIZE;
}
else if(itemType == BigWigSectionHeader.WigItemType.VarStep){
startBase = lbdis.readInt();
endBase = startBase + itemSpan;
value = lbdis.readFloat();
sectionDataSize += BigWigSectionHeader.VARSTEP_ITEM_SIZE;
}
else if(itemType == BigWigSectionHeader.WigItemType.BedGraph){
startBase = lbdis.readInt();
endBase = lbdis.readInt();
value = lbdis.readFloat();
sectionDataSize += BigWigSectionHeader.BEDGRAPH_ITEM_SIZE;
}
}
else { // byte order is high to low
if(itemType == BigWigSectionHeader.WigItemType.FixedStep){
startBase = chromStart;
endBase = startBase + itemSpan;
value = dis.readFloat();
chromStart = startBase + itemStep;
sectionDataSize += BigWigSectionHeader.FIXEDSTEP_ITEM_SIZE;
}
else if(itemType == BigWigSectionHeader.WigItemType.VarStep){
startBase = dis.readInt();
endBase = startBase + itemSpan;
value = dis.readFloat();
sectionDataSize += BigWigSectionHeader.VARSTEP_ITEM_SIZE;
}
else if(itemType == BigWigSectionHeader.WigItemType.BedGraph){
startBase = dis.readInt();
endBase = dis.readInt();
value = dis.readFloat();
sectionDataSize += BigWigSectionHeader.BEDGRAPH_ITEM_SIZE;
}
}
// contained leaf region items are always added - otherwise test conditions
if(leafHitValue == 0) {
WigItem bbItem = new WigItem(itemIndex, chromosome, startBase, endBase, value);
wigItemList.add(bbItem);
}
else {
itemRegion = new RPChromosomeRegion(chromID, startBase, chromID, endBase);
int itemHitValue = itemRegion.compareRegions(selectionRegion);
// hitValue < 2 needed for intersection; hitValue < 1 needed for contained = true
if(itemHitValue == 0 || !contained && Math.abs(itemHitValue) < 2) {
WigItem bbItem = new WigItem(itemIndex, chromosome, startBase, endBase, value);
wigItemList.add(bbItem);
}
}
}
}catch(IOException ex) {
log.error("Read error for Wig section item " + itemIndex);
throw new RuntimeException("Read error for Wig section item " + itemIndex);
}
return sectionDataSize;
}
/*
* Method prints out the data items for this Wig section.
* */
public void print() {
log.debug("Wig section for leaf item has a data size = " + sectionDataSize);
wigSectionHeader.print();
}
}
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