From 46c14ec63fde1d2d35e61eb801799d470ad44790 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 25 Mar 2010 17:41:22 +0000
Subject: [PATCH] New, much less memory intensive implementation of BAM file
 sharding.  Streams indices together with the expectation that bins will be
 present in the bin sparse array, which avoids the problem of having to hold
 the sparse bin array stored in every BAM file index in memory at the same
 time.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3075 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../BlockDelimitedReadShardStrategy.java      |  18 +-
 .../IndexDelimitedLocusShardStrategy.java     |  10 +-
 .../datasources/shards/IntervalSharder.java   | 519 ++++++++++--------
 ... picard-private-parts-1333-sharding-4.jar} | Bin 288615 -> 288615 bytes
 ... picard-private-parts-1333-sharding-4.xml} |   2 +-
 ...rding.jar => picard-1.16.364-sharding.jar} | Bin 407397 -> 407397 bytes
 ...rding.xml => picard-1.16.364-sharding.xml} |   2 +-
 ...sharding.jar => sam-1.16.364-sharding.jar} | Bin 453399 -> 456344 bytes
 ...sharding.xml => sam-1.16.364-sharding.xml} |   2 +-
 9 files changed, 319 insertions(+), 234 deletions(-)
 rename settings/repository/edu.mit.broad/{picard-private-parts-1333-sharding-3.jar => picard-private-parts-1333-sharding-4.jar} (94%)
 rename settings/repository/edu.mit.broad/{picard-private-parts-1333-sharding-3.xml => picard-private-parts-1333-sharding-4.xml} (55%)
 rename settings/repository/net.sf/{picard-1.16.363-sharding.jar => picard-1.16.364-sharding.jar} (95%)
 rename settings/repository/net.sf/{picard-1.16.363-sharding.xml => picard-1.16.364-sharding.xml} (76%)
 rename settings/repository/net.sf/{sam-1.16.363-sharding.jar => sam-1.16.364-sharding.jar} (94%)
 rename settings/repository/net.sf/{sam-1.16.363-sharding.xml => sam-1.16.364-sharding.xml} (52%)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java
index 032c93b54..12feb4c74 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java
@@ -27,7 +27,12 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
     /**
      * The data source used to shard.
      */
-    protected final BlockDrivenSAMDataSource dataSource;
+    private final BlockDrivenSAMDataSource dataSource;
+
+    /**
+     * The intervals to be processed.
+     */
+    private final GenomeLocSortedSet locations;
 
     /**
      * The cached shard to be returned next.  Prefetched in the peekable iterator style.
@@ -63,10 +68,13 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
 
         this.dataSource = (BlockDrivenSAMDataSource)dataSource;
         this.position = this.dataSource.getCurrentPosition();
-        if(locations != null)
-            filePointers.addAll(IntervalSharder.shardIntervals(this.dataSource,locations.toList()));
+        this.locations = locations;
+
+        if(locations != null)
+            filePointerIterator = IntervalSharder.shardIntervals(this.dataSource,locations.toList());
+        else
+            filePointerIterator = filePointers.iterator();
 
-        filePointerIterator = filePointers.iterator();
         if(filePointerIterator.hasNext())
             currentFilePointer = filePointerIterator.next();
 
@@ -99,7 +107,7 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
         nextShard = null;
         SamRecordFilter filter = null;
 
-        if(!filePointers.isEmpty()) {
+        if(locations != null) {
             Map<SAMReaderID,List<Chunk>> selectedReaders = new HashMap<SAMReaderID,List<Chunk>>();
             while(selectedReaders.size() == 0 && currentFilePointer != null) {
                 shardPosition = currentFilePointer.chunks;
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
index d428064d3..20c44b994 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
@@ -12,7 +12,6 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 import java.util.*;
 
 import net.sf.samtools.Chunk;
-import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMSequenceRecord;
 
@@ -51,9 +50,6 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
      */
     private final BlockDrivenSAMDataSource reads;
 
-    /** our storage of the genomic locations they'd like to shard over */
-    private final List<FilePointer> filePointers = new ArrayList<FilePointer>();
-
     /**
      * An iterator through the available file pointers.
      */
@@ -90,13 +86,13 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
             else
                 intervals = locations.toList();
 
-
             this.reads = (BlockDrivenSAMDataSource)reads;
-            filePointers.addAll(IntervalSharder.shardIntervals(this.reads,intervals));
+            this.filePointerIterator = IntervalSharder.shardIntervals(this.reads,intervals);
         }
         else {
             final int maxShardSize = 100000;
             this.reads = null;
+            List<FilePointer> filePointers = new ArrayList<FilePointer>();
             if(locations == null) {
                 for(SAMSequenceRecord refSequenceRecord: reference.getSequenceDictionary().getSequences()) {
                     for(int shardStart = 1; shardStart <= refSequenceRecord.getSequenceLength(); shardStart += maxShardSize) {
@@ -109,9 +105,9 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
                 for(GenomeLoc interval: locations)
                     filePointers.add(new FilePointer(interval));
             }
+            filePointerIterator = filePointers.iterator();
         }
 
-        filePointerIterator = filePointers.iterator();        
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
index 91520f842..311c8a94f 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
@@ -1,9 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.BlockDrivenSAMDataSource;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 
@@ -19,192 +16,113 @@ import net.sf.picard.util.PeekableIterator;
  * @version 0.1
  */
 public class IntervalSharder {
-    protected static List<FilePointer> shardIntervals(final BlockDrivenSAMDataSource dataSource, final List<GenomeLoc> loci) {
-        Map<SAMReaderID,List<FilePointer>> filePointersByReader = new HashMap<SAMReaderID,List<FilePointer>>();
-        for(SAMReaderID id: dataSource.getReaderIDs()) {
-            PreloadedBAMFileIndex index = dataSource.getIndex(id);
-            // Gather bins for the given loci, splitting loci as necessary so that each falls into exactly one lowest-level bin.\
-            filePointersByReader.put(id,shardIntervalsOverIndex(dataSource,id,index,loci,index.getNumIndexLevels()-1));
-            index.close();
-        }
-        return combineFilePointers(filePointersByReader);
+    public static Iterator<FilePointer> shardIntervals(final BlockDrivenSAMDataSource dataSource, final List<GenomeLoc> loci) {
+        return new FilePointerIterator(dataSource,loci);
     }
 
     /**
-     * Combine adjacent file pointers into a structure that can be streamed in.
-     * @param filePointersByReader File pointers broken down by reader.
-     * @return A large structure of file pointers.
+     * A lazy-loading iterator over file pointers.
      */
-    private static List<FilePointer> combineFilePointers(Map<SAMReaderID,List<FilePointer>> filePointersByReader) {
-        PeekableIterator<FilePointer> mergingIterator = new PeekableIterator<FilePointer>(new FilePointerMergingIterator(filePointersByReader));
+    private static class FilePointerIterator implements Iterator<FilePointer> {
+        final BlockDrivenSAMDataSource dataSource;
+        final PeekableIterator<GenomeLoc> locusIterator;
+        final Queue<FilePointer> cachedFilePointers = new LinkedList<FilePointer>();
 
-        List<FilePointer> overlappingFilePointers = new ArrayList<FilePointer>();
-        List<FilePointer> mergedFilePointers = new ArrayList<FilePointer>();
-
-        while(mergingIterator.hasNext()) {
-            GenomeLoc bounds = null;
-
-            // Load up a segment where file pointers overlap
-            while(mergingIterator.hasNext() && (overlappingFilePointers.size() == 0 || mergingIterator.peek().getBounds().overlapsP(bounds))) {
-                FilePointer filePointer = mergingIterator.next();
-                if(bounds != null)
-                    bounds = GenomeLocParser.createGenomeLoc(bounds.getContig(),
-                            Math.min(bounds.getStart(),filePointer.getBounds().getStart()),
-                            Math.max(bounds.getStop(),filePointer.getBounds().getStop()));
-                else
-                    bounds = filePointer.getBounds();
-                overlappingFilePointers.add(filePointer);
-            }
-
-            // determine the complete set of unique locations defining this set.
-            List<GenomeLoc> overlappingLocations = new ArrayList<GenomeLoc>();
-            for(FilePointer filePointer: overlappingFilePointers)
-                overlappingLocations.addAll(filePointer.locations);
-            Collections.sort(overlappingLocations);
-            overlappingLocations = GenomeLocSortedSet.mergeOverlappingLocations(overlappingLocations);
-
-            while(!overlappingLocations.isEmpty()) {
-                long overlapStart = overlappingLocations.get(0).getStart();
-                long overlapStop = overlappingLocations.get(overlappingLocations.size()-1).getStop();
-
-                for(FilePointer overlappingFilePointer: overlappingFilePointers) {
-                    if(overlappingFilePointer.getBounds().getStop() < overlapStart)
-                        continue;
-                    if(overlappingFilePointer.getBounds().getStart() > overlapStart) overlapStop = Math.min(overlapStop,overlappingFilePointer.getBounds().getStart()-1);
-                    if(overlappingFilePointer.getBounds().getStop() < overlapStop) overlapStop = Math.min(overlapStop,overlappingFilePointer.getBounds().getStop());
-                }
-
-                // Find the overlapping genome locs.
-                List<GenomeLoc> segmentOverlap = new ArrayList<GenomeLoc>();
-                for(GenomeLoc overlappingLocation: overlappingLocations) {
-                    if(overlappingLocation.getStop() <= overlapStop) {
-                        // segment is completely before end of overlap.
-                        segmentOverlap.add(overlappingLocation);
-                    }
-                    else if(overlappingLocation.getStart() <= overlapStop) {
-                        // segment is partially before end of overlap.
-                        segmentOverlap.add(GenomeLocParser.setStop(overlappingLocation,overlapStop));
-                        break;
-                    }
-                    else {
-                        // segment starts after overlap ends.
-                        break;
-                    }
-                }
-
-                // Trim the overlapping genome locs of the overlapping locations list.
-                while(!overlappingLocations.isEmpty() && overlappingLocations.get(0).getStart() <= overlapStop) {
-                    GenomeLoc location = overlappingLocations.remove(0);
-                    if(location.getStop() > overlapStop)
-                        overlappingLocations.add(0,GenomeLocParser.setStart(location,overlapStop+1));
-                }
-
-                // Merge together all file pointers that overlap with these bounds.
-                GenomeLoc overlapBounds = GenomeLocParser.createGenomeLoc(segmentOverlap.get(0).getContigIndex(),overlapStart,overlapStop);
-                FilePointer mergedFilePointer = null;
-                for(FilePointer overlappingFilePointer: overlappingFilePointers) {
-                    if(overlappingFilePointer.getBounds().overlapsP(overlapBounds))
-                        mergedFilePointer = overlappingFilePointer.merge(mergedFilePointer,segmentOverlap);
-                }
-
-                // Add the resulting file pointer and clear state.
-                mergedFilePointers.add(mergedFilePointer);
-            }
-
-            // reset
-            overlappingFilePointers.clear();
-        }
-
-        return mergedFilePointers;
-    }
-
-    private static class FilePointerMergingIterator implements Iterator<FilePointer> {
-        private PriorityQueue<PeekableIterator<FilePointer>> filePointerQueue;
-
-        public FilePointerMergingIterator(Map<SAMReaderID,List<FilePointer>> filePointers) {
-            filePointerQueue = new PriorityQueue<PeekableIterator<FilePointer>>(filePointers.size(),new FilePointerMergingComparator());
-            for(List<FilePointer> filePointersByReader: filePointers.values())
-                filePointerQueue.add(new PeekableIterator<FilePointer>(filePointersByReader.iterator()));
+        public FilePointerIterator(final BlockDrivenSAMDataSource dataSource, final List<GenomeLoc> loci) {
+            this.dataSource = dataSource;
+            locusIterator = new PeekableIterator<GenomeLoc>(loci.iterator());
+            advance();
         }
 
         public boolean hasNext() {
-            return !filePointerQueue.isEmpty();
+            return !cachedFilePointers.isEmpty();
         }
 
         public FilePointer next() {
-            if(!hasNext()) throw new NoSuchElementException("FilePointerMergingIterator is out of elements");
-            PeekableIterator<FilePointer> nextIterator = filePointerQueue.remove();
-            FilePointer nextFilePointer = nextIterator.next();
-            if(nextIterator.hasNext())
-                filePointerQueue.add(nextIterator);
-            return nextFilePointer;
+            if(!hasNext())
+                throw new NoSuchElementException("FilePointerIterator iteration is complete");
+            FilePointer filePointer = cachedFilePointers.remove();
+            if(cachedFilePointers.isEmpty())
+                advance();
+            return filePointer;
         }
 
-        public void remove() { throw new UnsupportedOperationException("Cannot remove from a merging iterator."); }
+        public void remove() {
+            throw new UnsupportedOperationException("Cannot remove from a FilePointerIterator");
+        }
 
-        private class FilePointerMergingComparator implements Comparator<PeekableIterator<FilePointer>> {
-            public int compare(PeekableIterator<FilePointer> lhs, PeekableIterator<FilePointer> rhs) {
-                if(!lhs.hasNext() && !rhs.hasNext()) return 0;
-                if(!rhs.hasNext()) return -1;
-                if(!lhs.hasNext()) return 1;
-                return lhs.peek().getBounds().compareTo(rhs.peek().getBounds());
+        private void advance() {
+            List<GenomeLoc> nextBatch = new ArrayList<GenomeLoc>();
+            String contig = null;
+
+            while(locusIterator.hasNext() && nextBatch.isEmpty()) {
+                contig = null;
+                while(locusIterator.hasNext() && (contig == null || locusIterator.peek().getContig().equals(contig))) {
+                    GenomeLoc nextLocus = locusIterator.next();
+                    contig = nextLocus.getContig();
+                    nextBatch.add(nextLocus);
+                }
             }
+
+            if(nextBatch.size() > 0)
+                cachedFilePointers.addAll(shardIntervalsOnContig(dataSource,contig,nextBatch));
         }
     }
-
-    private static List<FilePointer> shardIntervalsOverIndex(final BlockDrivenSAMDataSource dataSource, final SAMReaderID id, final PreloadedBAMFileIndex index, final List<GenomeLoc> loci, final int binsDeeperThan) {
+    
+    private static List<FilePointer> shardIntervalsOnContig(final BlockDrivenSAMDataSource dataSource, final String contig, final List<GenomeLoc> loci) {
         // Gather bins for the given loci, splitting loci as necessary so that each falls into exactly one lowest-level bin.
         List<FilePointer> filePointers = new ArrayList<FilePointer>();
         FilePointer lastFilePointer = null;
-        Bin lastBin = null;
+        BAMOverlap lastBAMOverlap = null;
+
+        Map<SAMReaderID,PreloadedBAMFileIndex> readerToIndexMap = new HashMap<SAMReaderID,PreloadedBAMFileIndex>();
+        BinMergingIterator binMerger = new BinMergingIterator();
+        for(SAMReaderID id: dataSource.getReaderIDs()) {
+            final SAMSequenceRecord referenceSequence = dataSource.getHeader(id).getSequence(contig);
+            final PreloadedBAMFileIndex index = dataSource.getIndex(id);
+            binMerger.addReader(id,
+                                index,
+                                referenceSequence.getSequenceIndex(),
+                                index.getBinsOverlapping(referenceSequence.getSequenceIndex(),1,referenceSequence.getSequenceLength()).iterator());
+            // Cache the reader for later data lookup.
+            readerToIndexMap.put(id,index);
+        }
+        PeekableIterator<BAMOverlap> binIterator = new PeekableIterator<BAMOverlap>(binMerger);
 
         for(GenomeLoc location: loci) {
-            // If crossing contigs, be sure to reset the filepointer that's been accumulating shard data.
-            if(lastFilePointer != null && lastFilePointer.referenceSequence != location.getContigIndex()) {
-                filePointers.add(lastFilePointer);
-                lastFilePointer = null;
-                lastBin = null;
-            }
+            if(!location.getContig().equals(contig))
+                throw new StingException("Location outside bounds of contig");
 
             int locationStart = (int)location.getStart();
             final int locationStop = (int)location.getStop();
 
-            List<Bin> bins = findBinsAtLeastAsDeepAs(index,getOverlappingBins(dataSource,id,index,location),binsDeeperThan);
+            // Advance to first bin.
+            while(binIterator.peek().stop < locationStart) 
+                binIterator.next();
 
-            // Recursive stopping condition -- algorithm is at the zero point and no bins have been found.
-            if(binsDeeperThan == 0 && bins.size() == 0) {
-                filePointers.add(new FilePointer(location));
-                continue;
-            }
-
-            // No bins found; step up a level and search again.
-            if(bins.size() == 0) {
-                if(lastFilePointer != null && lastFilePointer.locations.size() > 0) {
-                    filePointers.add(lastFilePointer);
-                    lastFilePointer = null;
-                    lastBin = null;
-                }
-
-                filePointers.addAll(shardIntervalsOverIndex(dataSource,id,index,Collections.singletonList(location),binsDeeperThan-1));
-                continue;
-            }
+            // Add all relevant bins to a list.  If the given bin extends beyond the end of the current interval, make
+            // sure the extending bin is not pruned from the list.
+            List<BAMOverlap> bamOverlaps = new ArrayList<BAMOverlap>();
+            while(binIterator.hasNext() && binIterator.peek().stop <= locationStop)
+                bamOverlaps.add(binIterator.next());
+            if(binIterator.hasNext() && binIterator.peek().start <= locationStop)
+                bamOverlaps.add(binIterator.peek());
 
             // Bins found; try to match bins with locations.
-            Collections.sort(bins);
-            Iterator<Bin> binIterator = bins.iterator();
+            Iterator<BAMOverlap> bamOverlapIterator = bamOverlaps.iterator();
 
             while(locationStop >= locationStart) {
-                int binStart = lastFilePointer!=null ? index.getFirstLocusInBin(lastBin) : 0;
-                int binStop = lastFilePointer!=null ? index.getLastLocusInBin(lastBin) : 0;
+                int binStart = lastFilePointer!=null ? lastFilePointer.overlap.start : 0;
+                int binStop =  lastFilePointer!=null ? lastFilePointer.overlap.stop : 0;
 
-                while(binStop < locationStart && binIterator.hasNext()) {
+                while(binStop < locationStart && bamOverlapIterator.hasNext()) {
                     if(lastFilePointer != null && lastFilePointer.locations.size() > 0)
                         filePointers.add(lastFilePointer);
 
-                    lastBin = binIterator.next();
-                    lastFilePointer = new FilePointer(id,lastBin.referenceSequence,getFilePointersBounding(index,lastBin));
-                    binStart = index.getFirstLocusInBin(lastBin);
-                    binStop = index.getLastLocusInBin(lastBin);
+                    lastBAMOverlap = bamOverlapIterator.next();
+                    lastFilePointer = new FilePointer(contig,lastBAMOverlap);
+                    binStart = lastFilePointer.overlap.start;
+                    binStop = lastFilePointer.overlap.stop;
                 }
 
                 if(locationStart < binStart) {
@@ -212,13 +130,13 @@ public class IntervalSharder {
                     if(lastFilePointer != null && lastFilePointer.locations.size() > 0) {
                         filePointers.add(lastFilePointer);
                         lastFilePointer = null;
-                        lastBin = null;
+                        lastBAMOverlap = null;
                     }
 
                     final int regionStop = Math.min(locationStop,binStart-1);
 
                     GenomeLoc subset = GenomeLocParser.createGenomeLoc(location.getContig(),locationStart,regionStop);
-                    filePointers.addAll(shardIntervalsOverIndex(dataSource,id,index,Collections.singletonList(subset),binsDeeperThan-1));
+                    lastFilePointer = new FilePointer(subset);
 
                     locationStart = regionStop + 1;
                 }
@@ -227,20 +145,21 @@ public class IntervalSharder {
                     if(lastFilePointer != null && lastFilePointer.locations.size() > 0) {
                         filePointers.add(lastFilePointer);
                         lastFilePointer = null;
-                        lastBin = null;
+                        lastBAMOverlap = null;
                     }
 
                     GenomeLoc subset = GenomeLocParser.createGenomeLoc(location.getContig(),locationStart,locationStop);
-                    filePointers.addAll(shardIntervalsOverIndex(dataSource,id,index,Collections.singletonList(subset),binsDeeperThan-1));
+                    filePointers.add(new FilePointer(subset));
 
                     locationStart = locationStop + 1;
                 }
                 else {
+                    if(lastFilePointer == null)
+                        throw new StingException("Illegal state: initializer failed to create cached file pointer.");
+
                     // The start of the region overlaps the bin.  Add the overlapping subset.
                     final int regionStop = Math.min(locationStop,binStop);
-                    lastFilePointer.addLocation(GenomeLocParser.createGenomeLoc(location.getContig(),
-                            locationStart,
-                            regionStop));
+                    lastFilePointer.addLocation(GenomeLocParser.createGenomeLoc(location.getContig(),locationStart,regionStop));
                     locationStart = regionStop + 1;
                 }
             }
@@ -249,48 +168,204 @@ public class IntervalSharder {
         if(lastFilePointer != null && lastFilePointer.locations.size() > 0)
             filePointers.add(lastFilePointer);
 
+        // Lookup the locations for every file pointer in the index.
+        for(SAMReaderID id: dataSource.getReaderIDs()) {
+            PreloadedBAMFileIndex index = readerToIndexMap.get(id);
+            for(FilePointer filePointer: filePointers)
+                filePointer.addChunks(id,index.getChunksOverlapping(filePointer.overlap.getBin(id)));
+            index.close();
+        }
+        
         return filePointers;
     }
 
-    private static List<Bin> findBinsAtLeastAsDeepAs(final PreloadedBAMFileIndex index, final List<Bin> bins, final int deepestBinLevel) {
-        List<Bin> deepestBins = new ArrayList<Bin>();
-        for(Bin bin: bins) {
-            if(index.getLevelForBin(bin) >= deepestBinLevel)
-                deepestBins.add(bin);
+    private static class BinMergingIterator implements Iterator<BAMOverlap> {
+        private PriorityQueue<BinQueueState> binQueue = new PriorityQueue<BinQueueState>();
+        private Queue<BAMOverlap> pendingOverlaps = new LinkedList<BAMOverlap>();
+
+        public void addReader(final SAMReaderID id, final PreloadedBAMFileIndex index, final int referenceSequence, Iterator<Bin> bins) {
+            binQueue.add(new BinQueueState(id,index,referenceSequence,new LowestLevelBinFilteringIterator(index,bins)));
+        }
+
+        public boolean hasNext() {
+            return pendingOverlaps.size() > 0 || !binQueue.isEmpty();
+        }
+
+        public BAMOverlap next() {
+            if(!hasNext())
+                throw new NoSuchElementException("No elements left in merging iterator");
+            if(pendingOverlaps.isEmpty())
+                advance();
+            return pendingOverlaps.remove();
+        }
+
+        public void advance() {
+            List<ReaderBin> bins = new ArrayList<ReaderBin>();
+            int boundsStart, boundsStop;
+
+            // Prime the pump
+            if(binQueue.isEmpty())
+                return;
+            bins.add(getNextBin());
+            boundsStart = bins.get(0).getStart();
+            boundsStop  = bins.get(0).getStop();
+
+            // Accumulate all the bins that overlap the current bin, in sorted order.
+            while(!binQueue.isEmpty() && peekNextBin().getStart() <= boundsStop) {
+                ReaderBin bin = getNextBin();
+                bins.add(bin);
+                boundsStart = Math.min(boundsStart,bin.getStart());
+                boundsStop = Math.max(boundsStop,bin.getStop());
+            }
+
+            List<Pair<Integer,Integer>> range = new ArrayList<Pair<Integer,Integer>>();
+            int start = bins.get(0).getStart();
+            int stop = bins.get(0).getStop();
+            while(start <= boundsStop) {
+                // Find the next stopping point.
+                for(ReaderBin bin: bins) {
+                    stop = Math.min(stop,bin.getStop());
+                    if(start < bin.getStart())
+                        stop = Math.min(stop,bin.getStart()-1);
+                }
+
+                range.add(new Pair<Integer,Integer>(start,stop));
+                // If the last entry added included the last element, stop.
+                if(stop >= boundsStop)
+                    break;
+
+                // Find the next start.
+                start = stop + 1;
+                for(ReaderBin bin: bins) {
+                    if(start >= bin.getStart() && start <= bin.getStop())
+                        break;
+                    else if(start < bin.getStart()) {
+                        start = bin.getStart();
+                        break;
+                    }
+                }
+            }
+
+            // Add the next series of BAM overlaps to the window.
+            for(Pair<Integer,Integer> window: range) {
+                BAMOverlap bamOverlap = new BAMOverlap(window.first,window.second);
+                for(ReaderBin bin: bins)
+                    bamOverlap.addBin(bin.id,bin.bin);
+                pendingOverlaps.add(bamOverlap);
+            }
+        }
+
+        public void remove() { throw new UnsupportedOperationException("Cannot remove from a merging iterator."); }
+
+        private ReaderBin peekNextBin() {
+            if(binQueue.isEmpty())
+                throw new NoSuchElementException("No more bins are available");
+            BinQueueState current = binQueue.peek();
+            return new ReaderBin(current.id,current.index,current.referenceSequence,current.bins.peek());
+        }
+
+        private ReaderBin getNextBin() {
+            if(binQueue.isEmpty())
+                throw new NoSuchElementException("No more bins are available");
+            BinQueueState current = binQueue.remove();
+            ReaderBin readerBin = new ReaderBin(current.id,current.index,current.referenceSequence,current.bins.next());
+            if(current.bins.hasNext())
+                binQueue.add(current);
+            return readerBin;
+        }
+
+        private class ReaderBin {
+            public final SAMReaderID id;
+            public final PreloadedBAMFileIndex index;
+            public final int referenceSequence;
+            public final Bin bin;
+
+            public ReaderBin(final SAMReaderID id, final PreloadedBAMFileIndex index, final int referenceSequence, final Bin bin) {
+                this.id = id;
+                this.index = index;
+                this.referenceSequence = referenceSequence;
+                this.bin = bin;
+            }
+
+            public int getStart() {
+                return index.getFirstLocusInBin(bin);
+            }
+
+            public int getStop() {
+                return index.getLastLocusInBin(bin);
+            }
+        }
+
+        private class BinQueueState implements Comparable<BinQueueState> {
+            public final SAMReaderID id;
+            public final PreloadedBAMFileIndex index;
+            public final int referenceSequence;
+            public final PeekableIterator<Bin> bins;
+
+            public BinQueueState(final SAMReaderID id, final PreloadedBAMFileIndex index, final int referenceSequence, final Iterator<Bin> bins) {
+                this.id = id;
+                this.index = index;
+                this.referenceSequence = referenceSequence;
+                this.bins = new PeekableIterator<Bin>(bins);
+            }
+
+            public int compareTo(BinQueueState other) {
+                if(!this.bins.hasNext() && !other.bins.hasNext()) return 0;
+                if(!this.bins.hasNext()) return -1;
+                if(!this.bins.hasNext()) return 1;
+
+                int thisStart = this.index.getFirstLocusInBin(this.bins.peek());
+                int otherStart = other.index.getFirstLocusInBin(other.bins.peek());
+
+                // Straight integer subtraction works here because lhsStart, rhsStart always positive.
+                if(thisStart != otherStart)
+                    return thisStart - otherStart;
+
+                int thisStop = this.index.getLastLocusInBin(this.bins.peek());
+                int otherStop = other.index.getLastLocusInBin(other.bins.peek());
+
+                // Straight integer subtraction works here because lhsStop, rhsStop always positive.
+                return thisStop - otherStop;
+            }
         }
-        return deepestBins;
     }
 
     /**
-     * Gets a list of the bins in each BAM file that overlap with the given interval list.
-     * @param location Location for which to determine the bin.
-     * @return A map of reader back to bin.
+     * Filters out bins not at the lowest level in the tree.
      */
-    private static List<Bin> getOverlappingBins(final BlockDrivenSAMDataSource dataSource, final SAMReaderID id, final PreloadedBAMFileIndex index, final GenomeLoc location) {
-        // All readers will have the same bin structure, so just use the first bin as an example.
-        final SAMFileHeader fileHeader = dataSource.getHeader(id);
-        int referenceIndex = fileHeader.getSequenceIndex(location.getContig());
-        if (referenceIndex != -1) {
-            return index.getBinsContaining(referenceIndex,(int)location.getStart(),(int)location.getStop());
+    private static class LowestLevelBinFilteringIterator implements Iterator<Bin> {
+        private PreloadedBAMFileIndex index;
+        private Iterator<Bin> wrappedIterator;
+
+        private Bin nextBin;
+
+        public LowestLevelBinFilteringIterator(final PreloadedBAMFileIndex index, Iterator<Bin> iterator) {
+            this.index = index;
+            this.wrappedIterator = iterator;
+            advance();
         }
-        return Collections.emptyList();
-    }
 
-    /**
-     * Gets the file pointers bounded by this bin, grouped by the reader of origination.
-     * @param bin The bin for which to load data.
-     * @return A map of the file pointers bounding the bin.
-     */
-    private static List<Chunk> getFilePointersBounding(final PreloadedBAMFileIndex index, final Bin bin) {
-        if(bin != null) {
-            List<Chunk> chunks = index.getSearchBins(bin);
-            return chunks != null ? chunks : Collections.<Chunk>emptyList();
+        public boolean hasNext() {
+            return nextBin != null;
         }
-        else
-            return Collections.emptyList();
-    }
 
+        public Bin next() {
+            Bin bin = nextBin;
+            advance();
+            return bin;
+        }
 
+        public void remove() { throw new UnsupportedOperationException("Remove operation is not supported"); }
+
+        private void advance() {
+            nextBin = null;
+            while(wrappedIterator.hasNext() && nextBin == null) {
+                Bin bin = wrappedIterator.next();
+                if(index.getLevelForBin(bin) == index.getNumIndexLevels()-1)
+                    nextBin = bin;
+            }
+        }
+    }    
 }
 
 /**
@@ -298,47 +373,53 @@ public class IntervalSharder {
  */
 class FilePointer {
     protected final Map<SAMReaderID,List<Chunk>> chunks = new HashMap<SAMReaderID,List<Chunk>>();
-    protected final int referenceSequence;
+    protected final String referenceSequence;
+    protected final BAMOverlap overlap;
     protected final List<GenomeLoc> locations;
 
-    public FilePointer(SAMReaderID id, int referenceSequence, List<Chunk> chunks) {
-        this.referenceSequence = referenceSequence;
-        this.chunks.put(id,chunks);
-        this.locations = new ArrayList<GenomeLoc>();
-    }
-
-    public FilePointer(GenomeLoc location) {
-        referenceSequence = location.getContigIndex();
+    public FilePointer(final GenomeLoc location) {
+        referenceSequence = location.getContig();
+        overlap = null;
         locations = Collections.singletonList(location);
     }
 
-    /**
-     * Private constructor for merge operation.
-     * @param referenceSequence Sequence to merge.
-     * @param locations Merged locations.
-     */
-    private FilePointer(final int referenceSequence, final List<GenomeLoc> locations) {
+    public FilePointer(final String referenceSequence,final BAMOverlap overlap) {
         this.referenceSequence = referenceSequence;
-        this.locations = locations;
-    }
-
-    public FilePointer merge(FilePointer other, List<GenomeLoc> locations) {
-        FilePointer merged = new FilePointer(referenceSequence,locations);
-        merged.chunks.putAll(this.chunks);
-        if(other != null)
-            merged.chunks.putAll(other.chunks);
-        return merged;
+        this.overlap = overlap;
+        this.locations = new ArrayList<GenomeLoc>();
     }
 
     public void addLocation(GenomeLoc location) {
         locations.add(location);
     }
 
-    public GenomeLoc getBounds() {
-        final long boundaryStart = locations.get(0).getStart();
-        final long boundaryStop = locations.get(locations.size()-1).getStop();
-        return GenomeLocParser.createGenomeLoc(locations.get(0).getContigIndex(),boundaryStart,boundaryStop);    
+    public void addChunks(SAMReaderID id, List<Chunk> chunks) {
+        this.chunks.put(id,chunks);
+    }
+}
+
+/**
+ * Models a bin at which all BAM files in the merged input stream overlap.
+ */
+class BAMOverlap {
+    public final int start;
+    public final int stop;
+
+    private final Map<SAMReaderID,Bin> bins = new HashMap<SAMReaderID,Bin>();
+
+    public BAMOverlap(final int start, final int stop) {
+        this.start = start;
+        this.stop = stop;
+    }
+
+    public void addBin(final SAMReaderID id, final Bin bin) {
+        bins.put(id,bin);
+    }
+
+    public Bin getBin(final SAMReaderID id) {
+        return bins.get(id);
     }
 }
 
 
+
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.jar b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-4.jar
similarity index 94%
rename from settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.jar
rename to settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-4.jar
index 05ba590d337625b7415254bae1bbcb3b96596b54..f8fc13d6d1d6c2f9d9c8d04154cc873cb97d0244 100644
GIT binary patch
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diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.xml b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-4.xml
similarity index 55%
rename from settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.xml
rename to settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-4.xml
index 1b36b12ab..acccf2e28 100644
--- a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.xml
+++ b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-4.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1333-sharding-3" status="integration" publication="20100323163000" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1333-sharding-4" status="integration" publication="20100324095800" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.16.363-sharding.jar b/settings/repository/net.sf/picard-1.16.364-sharding.jar
similarity index 95%
rename from settings/repository/net.sf/picard-1.16.363-sharding.jar
rename to settings/repository/net.sf/picard-1.16.364-sharding.jar
index 60f977b53b5fff20ae66d6621ca0300ef5c34cf4..fc60bbb51dee15abb0bb487843e1fbc5fac80975 100644
GIT binary patch
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diff --git a/settings/repository/net.sf/picard-1.16.363-sharding.xml b/settings/repository/net.sf/picard-1.16.364-sharding.xml
similarity index 76%
rename from settings/repository/net.sf/picard-1.16.363-sharding.xml
rename to settings/repository/net.sf/picard-1.16.364-sharding.xml
index 31c6ab92b..b731a711d 100644
--- a/settings/repository/net.sf/picard-1.16.363-sharding.xml
+++ b/settings/repository/net.sf/picard-1.16.364-sharding.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.16.363-sharding" status="release" />
+    <info organisation="net.sf" module="picard" revision="1.16.364-sharding" status="release" />
 </ivy-module>
diff --git a/settings/repository/net.sf/sam-1.16.363-sharding.jar b/settings/repository/net.sf/sam-1.16.364-sharding.jar
similarity index 94%
rename from settings/repository/net.sf/sam-1.16.363-sharding.jar
rename to settings/repository/net.sf/sam-1.16.364-sharding.jar
index 3ebadb087864b1fcdc736f939f74d3ca50f376bc..7453d10ea71115c8532d0c77df34cdd5913dd036 100644
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diff --git a/settings/repository/net.sf/sam-1.16.363-sharding.xml b/settings/repository/net.sf/sam-1.16.364-sharding.xml
similarity index 52%
rename from settings/repository/net.sf/sam-1.16.363-sharding.xml
rename to settings/repository/net.sf/sam-1.16.364-sharding.xml
index cc08fdd9e..598c75488 100644
--- a/settings/repository/net.sf/sam-1.16.363-sharding.xml
+++ b/settings/repository/net.sf/sam-1.16.364-sharding.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.16.363-sharding" status="release" />
+    <info organisation="net.sf" module="sam" revision="1.16.364-sharding" status="release" />
 </ivy-module>