88 lines
2.8 KiB
Java
88 lines
2.8 KiB
Java
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package net.sf.samtools;
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import java.util.*;
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/**
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* Adapts a list of BAM blocks to BAM chunks.
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*
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* @author mhanna
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* @version 0.1
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*/
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public class BAMChunkIterator implements Iterator<Chunk> {
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/**
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* The wrapped chunk iterator.
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*/
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private final BAMBlockIterator blockIterator;
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/**
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* List of prefetched segments. If prefetchedSegments is
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* empty, this should mean that there's nothing left in the queue.
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*/
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private Queue<BlockSegment> prefetchedSegments;
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/**
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* List of chunks to filter out of the final chunk list.
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*/
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private final Queue<Chunk> filters;
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/**
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* Creates a new chunk iterator wrapping the given block, optionally filtering
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* out a list of chunks from those blocks.
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* TODO: This class is too smart. Wrap filtering functionality in another class.
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* @param blockIterator block iterator to wrap.
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* @param filters List of chunks to filter out of the given input stream.
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*/
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public BAMChunkIterator(BAMBlockIterator blockIterator, List<Chunk> filters) {
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this.blockIterator = blockIterator;
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this.prefetchedSegments = new LinkedList<BlockSegment>();
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this.filters = new PriorityQueue<Chunk>(filters);
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}
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/**
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* Is a next chunk available.
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* @return true if a next chunk is available; false otherwise.
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*/
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public boolean hasNext() {
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return !prefetchedSegments.isEmpty();
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}
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/**
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* Returns the next chunk in the list.
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* @return Next block, adapted to a chunk.
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*/
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public Chunk next() {
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if(prefetchedSegments.isEmpty())
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throw new NoSuchElementException("BAMChunkIterator is exhausted.");
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// TODO: Maybe tie together adjacent chunks together?
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Chunk nextChunk = prefetchedSegments.remove().toChunk();
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seedNextSegments();
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return nextChunk;
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}
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/**
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* @throws UnsupportedOperationException always.
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*/
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public void remove() {
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throw new UnsupportedOperationException("Cannot remove from a BAM chunk iterator");
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}
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/**
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* Seed the next value or set of values for the iterator, if necessary.
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*/
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private void seedNextSegments() {
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while(prefetchedSegments.isEmpty() && blockIterator.hasNext()) {
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// Add the new segments to the prefetch...
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prefetchedSegments.add(new BlockSegment(blockIterator.next()));
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// And iteratively subtract the filtering chunks.
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for(Chunk filter: filters) {
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Queue<BlockSegment> filteredBlockSegments = new LinkedList<BlockSegment>();
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for(BlockSegment blockSegment: prefetchedSegments)
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filteredBlockSegments.addAll(blockSegment.minus(filter));
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prefetchedSegments = filteredBlockSegments;
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}
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}
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}
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}
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