Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/*
* The MIT License
*
* Copyright (c) 2009 The 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 htsjdk.samtools;
import htsjdk.samtools.seekablestream.SeekableStream;
import java.io.File;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.List;
/**
* Class for reading BAM file indices, caching each contig as it's loaded and
* dropping values when the next contig is loaded.
*/
class CachingBAMFileIndex extends AbstractBAMFileIndex implements BrowseableBAMIndex
{
// Since null is a valid return value for this index, it's possible to have lastReferenceIndex != null and
// lastReference == null, this is effectively caching the return value null
private Integer lastReferenceIndex = null;
private BAMIndexContent lastReference = null;
private long cacheHits = 0;
private long cacheMisses = 0;
public CachingBAMFileIndex(final File file, final SAMSequenceDictionary dictionary) {
super(file, dictionary);
}
public CachingBAMFileIndex(final SeekableStream stream, final SAMSequenceDictionary dictionary) {
super(stream, dictionary);
}
public CachingBAMFileIndex(final File file, final SAMSequenceDictionary dictionary, final boolean useMemoryMapping) {
super(file, dictionary, useMemoryMapping);
}
/**
* Get list of regions of BAM file that may contain SAMRecords for the given range
* @param referenceIndex sequence of desired SAMRecords
* @param startPos 1-based start of the desired interval, inclusive
* @param endPos 1-based end of the desired interval, inclusive
* @return the virtual file position. Each pair is the first and last virtual file position
* in a range that can be scanned to find SAMRecords that overlap the given positions.
* May return null if there is no content overlapping the region.
*/
@Override
public BAMFileSpan getSpanOverlapping(final int referenceIndex, final int startPos, final int endPos) {
final BAMIndexContent queryResults = getQueryResults(referenceIndex);
if(queryResults == null)
return null;
final List chunkList = queryResults.getChunksOverlapping(startPos, endPos);
if (chunkList == null) return null;
return new BAMFileSpan(chunkList);
}
/**
* Get a list of bins in the BAM file that may contain SAMRecords for the given range.
* @param referenceIndex sequence of desired SAMRecords
* @param startPos 1-based start of the desired interval, inclusive
* @param endPos 1-based end of the desired interval, inclusive
* @return a list of bins that contain relevant data.
*/
@Override
public BinList getBinsOverlapping(final int referenceIndex, final int startPos, final int endPos) {
final BitSet regionBins = GenomicIndexUtil.regionToBins(startPos, endPos);
if (regionBins == null) {
return null;
}
return new BinList(referenceIndex,regionBins);
}
/**
* Perform an overlapping query of all bins bounding the given location.
* @param bin The bin over which to perform an overlapping query.
* @return The file pointers
*/
@Override
public BAMFileSpan getSpanOverlapping(final Bin bin) {
if(bin == null)
return null;
final int referenceSequence = bin.getReferenceSequence();
final BAMIndexContent indexQuery = getQueryResults(referenceSequence);
if(indexQuery == null)
return null;
final int binLevel = getLevelForBin(bin);
final int firstLocusInBin = getFirstLocusInBin(bin);
// Add the specified bin to the tree if it exists.
final List binTree = new ArrayList<>();
if(indexQuery.containsBin(bin))
binTree.add(indexQuery.getBins().getBin(bin.getBinNumber()));
int currentBinLevel = binLevel;
while(--currentBinLevel >= 0) {
final int binStart = getFirstBinInLevel(currentBinLevel);
final int binWidth = getMaxAddressibleGenomicLocation()/getLevelSize(currentBinLevel);
final int binNumber = firstLocusInBin/binWidth + binStart;
final Bin parentBin = indexQuery.getBins().getBin(binNumber);
if(parentBin != null && indexQuery.containsBin(parentBin))
binTree.add(parentBin);
}
List chunkList = new ArrayList();
for(final Bin coveringBin: binTree) {
for(final Chunk chunk: coveringBin.getChunkList())
chunkList.add(chunk.clone());
}
final int start = getFirstLocusInBin(bin);
chunkList = Chunk.optimizeChunkList(chunkList,indexQuery.getLinearIndex().getMinimumOffset(start));
return new BAMFileSpan(chunkList);
}
/**
* Looks up the cached BAM query results if they're still in the cache and not expired. Otherwise,
* retrieves the cache results from disk.
* @param referenceIndex The reference to load. CachingBAMFileIndex only stores index data for entire references.
* @return The index information for this reference or null if no index information is available for the given index.
*/
@Override
protected BAMIndexContent getQueryResults(final int referenceIndex) {
// If this query is for the same reference index as the last query, return it.
// This compares a boxed Integer to an int with == which is ok because the Integer will be unboxed to the primitive value
if(lastReferenceIndex!=null && lastReferenceIndex == referenceIndex){
cacheHits++;
return lastReference;
}
// If not attempt to load it from disk.
final BAMIndexContent queryResults = query(referenceIndex,1,-1);
cacheMisses++;
lastReferenceIndex = referenceIndex;
lastReference = queryResults;
return lastReference;
}
public long getCacheHits() {
return cacheHits;
}
public long getCacheMisses() {
return cacheMisses;
}
}
