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Bug fix: was tracking state across BAMs that should've been tracked per-BAM. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5358 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-03-02 17:32:06 +00:00
parent bafa61c1fe
commit bef83b8b09
1 changed files with 15 additions and 16 deletions
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29
java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
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@ -31,13 +31,12 @@ import net.sf.samtools.GATKChunk;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.HashMap;
import java.util.Collections;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException; import java.util.NoSuchElementException;
/** /**
@ -104,13 +103,13 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
for(SAMReaderID reader: dataSource.getReaderIDs()) { for(SAMReaderID reader: dataSource.getReaderIDs()) {
GATKBAMIndex index = (GATKBAMIndex)dataSource.getIndex(reader); GATKBAMIndex index = (GATKBAMIndex)dataSource.getIndex(reader);
BinTree binTree = getNextOverlappingBinTree((GATKBAMIndex)dataSource.getIndex(reader),currentLocus); BinTree binTree = getNextOverlappingBinTree(reader,(GATKBAMIndex)dataSource.getIndex(reader),currentLocus);
if(binTree != null) { if(binTree != null) {
coveredRegionStart = Math.max(coveredRegionStart,binTree.getStart()); coveredRegionStart = Math.max(coveredRegionStart,binTree.getStart());
coveredRegionStop = Math.min(coveredRegionStop,binTree.getStop()); coveredRegionStop = Math.min(coveredRegionStop,binTree.getStop());
coveredRegion = loci.getGenomeLocParser().createGenomeLoc(currentLocus.getContig(),coveredRegionStart,coveredRegionStop); coveredRegion = loci.getGenomeLocParser().createGenomeLoc(currentLocus.getContig(),coveredRegionStart,coveredRegionStop);
GATKBAMFileSpan fileSpan = generateFileSpan(index,binTree,currentLocus); GATKBAMFileSpan fileSpan = generateFileSpan(reader,index,binTree,currentLocus);
nextFilePointer.addFileSpans(reader,fileSpan); nextFilePointer.addFileSpans(reader,fileSpan);
} }
} }
@ -149,28 +148,28 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
/** /**
* The last reference sequence processed by this iterator. * The last reference sequence processed by this iterator.
*/ */
private int lastReferenceSequenceLoaded = -1; private Map<SAMReaderID,Integer> lastReferenceSequenceLoaded = new HashMap<SAMReaderID,Integer>();
/** /**
* The stateful iterator used to progress through the genoem. * The stateful iterator used to progress through the genoem.
*/ */
private PeekableIterator<BinTree> binTreeIterator = null; private Map<SAMReaderID, PeekableIterator<BinTree>> binTreeIterators = new HashMap<SAMReaderID, PeekableIterator<BinTree>>();
/** /**
* Get the next overlapping tree of bins associated with the given BAM file. * Get the next overlapping tree of bins associated with the given BAM file.
* @param index BAM index representation. * @param index BAM index representation.
* @param locus Locus for which to grab the bin tree, if available. * @param locus Locus for which to grab the bin tree, if available.
* @return The BinTree overlapping the given locus. * @return The BinTree overlapping the given locus.
*/ */
private BinTree getNextOverlappingBinTree(final GATKBAMIndex index, final GenomeLoc locus) { private BinTree getNextOverlappingBinTree(final SAMReaderID reader, final GATKBAMIndex index, final GenomeLoc locus) {
// Stale reference sequence or first invocation. (Re)create the binTreeIterator. // Stale reference sequence or first invocation. (Re)create the binTreeIterator.
if(locus.getContigIndex() != lastReferenceSequenceLoaded) { if(!lastReferenceSequenceLoaded.containsKey(reader) || lastReferenceSequenceLoaded.get(reader) != locus.getContigIndex()) {
if(binTreeIterator != null) if(binTreeIterators.containsKey(reader))
binTreeIterator.close(); binTreeIterators.get(reader).close();
lastReferenceSequenceLoaded = locus.getContigIndex(); lastReferenceSequenceLoaded.put(reader,locus.getContigIndex());
binTreeIterator = new PeekableIterator<BinTree>(new BinTreeIterator(index,index.getIndexFile(),locus.getContigIndex())); binTreeIterators.put(reader,new PeekableIterator<BinTree>(new BinTreeIterator(index, index.getIndexFile(), locus.getContigIndex())));
} }
PeekableIterator<BinTree> binTreeIterator = binTreeIterators.get(reader);
if(!binTreeIterator.hasNext()) if(!binTreeIterator.hasNext())
return null; return null;
@ -195,7 +194,7 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
* @param initialRegion The region to employ when trimming the linear index. * @param initialRegion The region to employ when trimming the linear index.
* @return File span mapping to given region. * @return File span mapping to given region.
*/ */
private GATKBAMFileSpan generateFileSpan(final GATKBAMIndex index, final BinTree binTree, final GenomeLoc initialRegion) { private GATKBAMFileSpan generateFileSpan(final SAMReaderID reader, final GATKBAMIndex index, final BinTree binTree, final GenomeLoc initialRegion) {
List<GATKChunk> chunks = new ArrayList<GATKChunk>(binTree.size()); List<GATKChunk> chunks = new ArrayList<GATKChunk>(binTree.size());
for(GATKBin bin: binTree.getBins()) { for(GATKBin bin: binTree.getBins()) {
if(bin == null) if(bin == null)