Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of

Picard patch, including move of some of the Picard private classes we use to Picard public.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java

@@ -1,8 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
-import net.sf.samtools.Chunk;
+import net.sf.samtools.*;
-import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMRecord;
 import net.sf.picard.filter.SamRecordFilter;
 
 import java.util.List;
@@ -22,7 +20,7 @@ public interface BAMFormatAwareShard extends Shard {
      * Get the list of chunks delimiting this shard.
      * @return a list of chunks that contain data for this shard.
      */
-    public Map<SAMReaderID,List<Chunk>> getChunks();
+    public Map<SAMReaderID, BAMFileSpan> getFileSpans();
 
     /**
      * Returns true if this shard is meant to buffer reads, rather

java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java

@@ -1,8 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
-import net.sf.samtools.Chunk;
+import net.sf.samtools.*;
-import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMRecord;
 import net.sf.picard.filter.SamRecordFilter;
 
 import java.util.*;
@@ -28,7 +26,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
     /**
      * The data backing the next chunks to deliver to the traversal engine.
      */
-    private final Map<SAMReaderID,List<Chunk>> chunks;
+    private final Map<SAMReaderID,BAMFileSpan> fileSpans;
 
     /**
      * The reads making up this shard.
@@ -46,9 +44,9 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
      */
     private final Shard.ShardType shardType;        
 
-    public BlockDelimitedReadShard(Reads sourceInfo, Map<SAMReaderID,List<Chunk>> chunks, SamRecordFilter filter, Shard.ShardType shardType) {
+    public BlockDelimitedReadShard(Reads sourceInfo, Map<SAMReaderID,BAMFileSpan> fileSpans, SamRecordFilter filter, Shard.ShardType shardType) {
         this.sourceInfo = sourceInfo;
-        this.chunks = chunks;
+        this.fileSpans = fileSpans;
         this.filter = filter;
         this.shardType = shardType;
     }
@@ -58,6 +56,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
      * than just holding pointers to their locations.
      * @return True if this shard can buffer reads.  False otherwise.
      */
+    @Override
     public boolean buffersReads() {
         return true;
     }
@@ -66,6 +65,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
      * Returns true if the read buffer is currently full.
      * @return True if this shard's buffer is full (and the shard can buffer reads).
      */
+    @Override
     public boolean isBufferEmpty() {
         return reads.size() == 0;
     }    
@@ -74,6 +74,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
      * Returns true if the read buffer is currently full.
      * @return True if this shard's buffer is full (and the shard can buffer reads).
      */
+    @Override
     public boolean isBufferFull() {
         return reads.size() > BlockDelimitedReadShardStrategy.MAX_READS; 
     }
@@ -82,6 +83,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
      * Adds a read to the read buffer.
      * @param read Add a read to the internal shard buffer.
      */
+    @Override
     public void addRead(SAMRecord read) {
         // DO NOT validate that the buffer is full.  Paired read sharding will occasionally have to stuff another
         // read or two into the buffer.
@@ -92,10 +94,12 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
      * Creates an iterator over reads stored in this shard's read cache.
      * @return
      */
+    @Override
     public StingSAMIterator iterator() {
         return StingSAMIteratorAdapter.adapt(sourceInfo,reads.iterator());
     }
 
+    @Override
     public SamRecordFilter getFilter() {
         return filter;
     }
@@ -104,8 +108,9 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
      * Get the list of chunks delimiting this shard.
      * @return a list of chunks that contain data for this shard.
      */
-    public Map<SAMReaderID,List<Chunk>> getChunks() {
+    @Override
-        return Collections.unmodifiableMap(chunks);
+    public Map<SAMReaderID,BAMFileSpan> getFileSpans() {
+        return Collections.unmodifiableMap(fileSpans);
     }
 
     /**
@@ -123,15 +128,12 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
     @Override
     public String toString() {
         StringBuilder sb = new StringBuilder();
-        for(Map.Entry<SAMReaderID,List<Chunk>> entry: chunks.entrySet()) {
+        for(Map.Entry<SAMReaderID,BAMFileSpan> entry: fileSpans.entrySet()) {
             sb.append(entry.getKey());
             sb.append(": ");
-            for(Chunk chunk : entry.getValue()) {
+            sb.append(entry.getValue());
-                sb.append(chunk);
             sb.append(' ');
         }
-            sb.append(';');
-        }
         return sb.toString();
     }
 }

java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java

@@ -55,7 +55,7 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
     /**
      * Ending position of the last shard in the file.
      */
-    private Map<SAMReaderID,Chunk> position;
+    private Map<SAMReaderID,BAMFileSpan> position;
 
     /**
      * Create a new read shard strategy, loading read shards from the given BAM file.
@@ -103,26 +103,18 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
     }
 
     public void advance() {
-        Map<SAMReaderID,List<Chunk>> shardPosition = new HashMap<SAMReaderID,List<Chunk>>();
+        Map<SAMReaderID,BAMFileSpan> shardPosition = new HashMap<SAMReaderID,BAMFileSpan>();
         nextShard = null;
         SamRecordFilter filter = null;
 
         if(locations != null) {
-            Map<SAMReaderID,List<Chunk>> selectedReaders = new HashMap<SAMReaderID,List<Chunk>>();
+            Map<SAMReaderID,BAMFileSpan> selectedReaders = new HashMap<SAMReaderID,BAMFileSpan>();
             while(selectedReaders.size() == 0 && currentFilePointer != null) {
-                shardPosition = currentFilePointer.chunks;
+                shardPosition = currentFilePointer.fileSpans;
                 for(SAMReaderID id: shardPosition.keySet()) {
-                    List<Chunk> chunks = shardPosition.get(id);
+                    BAMFileSpan fileSpans = shardPosition.get(id).removeBefore(position.get(id));
-                    List<Chunk> selectedChunks = new ArrayList<Chunk>();
+                    if(!fileSpans.isEmpty())
-                    Chunk filePosition = position.get(id);
+                        selectedReaders.put(id,fileSpans);
-                    for(Chunk chunk: chunks)
-                        if(filePosition.getChunkStart() <= chunk.getChunkStart())
-                            selectedChunks.add(chunk);
-                        else if(filePosition.getChunkStart() > chunk.getChunkStart() && filePosition.getChunkStart() < chunk.getChunkEnd()) {
-                            selectedChunks.add(new Chunk(filePosition.getChunkStart(),chunk.getChunkEnd()));
-                    }
-                    if(selectedChunks.size() > 0)
-                        selectedReaders.put(id,selectedChunks);
                 }
 
                 if(selectedReaders.size() > 0) {
@@ -141,13 +133,7 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
             }
         }
         else {
-            // TODO: This level of processing should not be necessary.
+            BAMFormatAwareShard shard = new BlockDelimitedReadShard(dataSource.getReadsInfo(),position,filter,Shard.ShardType.READ);
-            shardPosition = new HashMap<SAMReaderID,List<Chunk>>();
-            for(Map.Entry<SAMReaderID,Chunk> entry: position.entrySet())
-                shardPosition.put(entry.getKey(),Collections.singletonList(entry.getValue()));
-            filter = null;
-
-            BAMFormatAwareShard shard = new BlockDelimitedReadShard(dataSource.getReadsInfo(),shardPosition,filter,Shard.ShardType.READ);
             dataSource.fillShard(shard);
             nextShard = !shard.isBufferEmpty() ? shard : null;
         }

java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java

@@ -4,9 +4,8 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
-import net.sf.samtools.Chunk;
-import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMRecord;
+import net.sf.samtools.BAMFileSpan;
 import net.sf.picard.filter.SamRecordFilter;
 
 import java.util.List;
@@ -45,7 +44,7 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa
     /**
      * A list of the chunks associated with this shard.
      */
-    private final Map<SAMReaderID,List<Chunk>> chunks;
+    private final Map<SAMReaderID, BAMFileSpan> fileSpans;
 
     /**
      * An IndexDelimitedLocusShard can be used either for LOCUS or LOCUS_INTERVAL shard types.
@@ -56,23 +55,24 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa
     /**
      * Create a new locus shard, divided by index.
      * @param intervals List of intervals to process.
-     * @param chunks Chunks associated with that interval.
+     * @param fileSpans File spans associated with that interval.
      * @param shardType Type of the shard; must be either LOCUS or LOCUS_INTERVAL.
      */
-    IndexDelimitedLocusShard(List<GenomeLoc> intervals, Map<SAMReaderID,List<Chunk>> chunks, ShardType shardType) {
+    IndexDelimitedLocusShard(List<GenomeLoc> intervals, Map<SAMReaderID,BAMFileSpan> fileSpans, ShardType shardType) {
         super(intervals);
-        this.chunks = chunks;
+        this.fileSpans = fileSpans;
         if(shardType != ShardType.LOCUS && shardType != ShardType.LOCUS_INTERVAL)
             throw new StingException("Attempted to create an IndexDelimitedLocusShard with invalid shard type: " + shardType);
         this.shardType = shardType;
     }
 
     /**
-     * Gets the chunks associated with this locus shard.
+     * Gets the file spans associated with this locus shard.
-     * @return A list of the chunks to use when retrieving locus data.
+     * @return A list of the file spans to use when retrieving locus data.
      */
-    public Map<SAMReaderID,List<Chunk>> getChunks() {
+    @Override
-        return chunks;
+    public Map<SAMReaderID,BAMFileSpan> getFileSpans() {
+        return fileSpans;
     }
 
     /**
@@ -80,36 +80,42 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa
      * than just holding pointers to their locations.
      * @return True if this shard can buffer reads.  False otherwise.
      */
+    @Override
     public boolean buffersReads() { return false; }
 
     /**
      * Returns true if the read buffer is currently full.
      * @return True if this shard's buffer is full (and the shard can buffer reads).
      */
+    @Override
     public boolean isBufferEmpty() { throw new UnsupportedOperationException("This shard does not buffer reads."); }    
 
     /**
      * Returns true if the read buffer is currently full.
      * @return True if this shard's buffer is full (and the shard can buffer reads).
      */
+    @Override
     public boolean isBufferFull() { throw new UnsupportedOperationException("This shard does not buffer reads."); }
 
     /**
      * Adds a read to the read buffer.
      * @param read Add a read to the internal shard buffer.
      */
+    @Override
     public void addRead(SAMRecord read) { throw new UnsupportedOperationException("This shard does not buffer reads."); }
 
     /**
      * Gets the iterator over the elements cached in the shard.
      * @return
      */
+    @Override
     public StingSAMIterator iterator() { throw new UnsupportedOperationException("This shard does not buffer reads."); }
 
     /**
      * Gets a filter testing for overlap of this read with the given shard.
      * @return A filter capable of filtering out reads outside a given shard.
      */
+    @Override
     public SamRecordFilter getFilter() {
         return new ReadOverlapFilter(loci);    
     }

java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java

@@ -11,9 +11,9 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 
 import java.util.*;
 
-import net.sf.samtools.Chunk;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMSequenceRecord;
+import net.sf.samtools.BAMFileSpan;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -126,8 +126,8 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
      */
     public IndexDelimitedLocusShard next() {
         FilePointer nextFilePointer = filePointerIterator.next();
-        Map<SAMReaderID,List<Chunk>> chunksBounding = nextFilePointer.chunks != null ? nextFilePointer.chunks : null;
+        Map<SAMReaderID, BAMFileSpan> fileSpansBounding = nextFilePointer.fileSpans != null ? nextFilePointer.fileSpans : null;
-        return new IndexDelimitedLocusShard(nextFilePointer.locations,chunksBounding,Shard.ShardType.LOCUS_INTERVAL);
+        return new IndexDelimitedLocusShard(nextFilePointer.locations,fileSpansBounding,Shard.ShardType.LOCUS_INTERVAL);
     }
 
     /** we don't support the remove command */

java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java

@@ -172,7 +172,7 @@ public class IntervalSharder {
         for(SAMReaderID id: dataSource.getReaderIDs()) {
             PreloadedBAMFileIndex index = readerToIndexMap.get(id);
             for(FilePointer filePointer: filePointers)
-                filePointer.addChunks(id,index.getChunksOverlapping(filePointer.overlap.getBin(id)));
+                filePointer.addFileSpans(id,index.getChunksOverlapping(filePointer.overlap.getBin(id)));
             index.close();
         }
         
@@ -372,7 +372,7 @@ public class IntervalSharder {
  * Represents a small section of a BAM file, and every associated interval.
  */
 class FilePointer {
-    protected final Map<SAMReaderID,List<Chunk>> chunks = new HashMap<SAMReaderID,List<Chunk>>();
+    protected final Map<SAMReaderID,BAMFileSpan> fileSpans = new HashMap<SAMReaderID,BAMFileSpan>();
     protected final String referenceSequence;
     protected final BAMOverlap overlap;
     protected final List<GenomeLoc> locations;
@@ -393,8 +393,8 @@ class FilePointer {
         locations.add(location);
     }
 
-    public void addChunks(SAMReaderID id, List<Chunk> chunks) {
+    public void addFileSpans(SAMReaderID id, BAMFileSpan fileSpan) {
-        this.chunks.put(id,chunks);
+        this.fileSpans.put(id,fileSpan);
     }
 }
 

java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java

@@ -6,7 +6,6 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import net.sf.samtools.*;
 import net.sf.samtools.util.CloseableIterator;
 import net.sf.picard.sam.SamFileHeaderMerger;
@@ -54,7 +53,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
     /**
      * How far along is each reader?
      */
-    private final Map<SAMReaderID,Chunk> readerPositions = new HashMap<SAMReaderID,Chunk>();
+    private final Map<SAMReaderID,BAMFileSpan> readerPositions = new HashMap<SAMReaderID,BAMFileSpan>();
 
     /**
      * Create a new block-aware SAM data source given the supplied read metadata.
@@ -139,7 +138,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
      * Retrieves the current position within the BAM file.
      * @return A mapping of reader to current position.
      */
-    public Map<SAMReaderID,Chunk> getCurrentPosition() {
+    public Map<SAMReaderID,BAMFileSpan> getCurrentPosition() {
         return readerPositions;
     }
 
@@ -183,7 +182,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
      * @param read The read to add to the shard.
      */
     private void addReadToBufferingShard(BAMFormatAwareShard shard,SAMReaderID id,SAMRecord read) {
-        Chunk endChunk = new Chunk(read.getCoordinates().getChunkEnd(),Long.MAX_VALUE);
+        BAMFileSpan endChunk = read.getFilePointer().getFilePointerFollowing();
         shard.addRead(read);
         readerPositions.put(id,endChunk);
     }
@@ -202,9 +201,13 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
         throw new StingException("Unable to find id for reader associated with read " + read.getReadName());
     }
 
+    /**
+     * Initialize the current reader positions 
+     * @param readers
+     */
     private void initializeReaderPositions(SAMReaders readers) {
         for(SAMReaderID id: getReaderIDs())
-            readerPositions.put(id,readers.getReader(id).getCurrentPosition());
+            readerPositions.put(id,readers.getReader(id).getStartOfDataSegment());
     }
 
     public StingSAMIterator seek(Shard shard) {
@@ -236,9 +239,9 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
     private StingSAMIterator getIterator(SAMReaders readers, BAMFormatAwareShard shard, boolean enableVerification) {
         Map<SAMFileReader,CloseableIterator<SAMRecord>> readerToIteratorMap = new HashMap<SAMFileReader,CloseableIterator<SAMRecord>>();
         for(SAMReaderID id: getReaderIDs()) {
-            if(shard.getChunks().get(id) == null)
+            if(shard.getFileSpans().get(id) == null)
                 continue;
-            CloseableIterator<SAMRecord> iterator = readers.getReader(id).iterator(shard.getChunks().get(id));
+            CloseableIterator<SAMRecord> iterator = readers.getReader(id).iterator(shard.getFileSpans().get(id));
             if(shard.getFilter() != null)
                 iterator = new FilteringIterator(iterator,shard.getFilter());
             readerToIteratorMap.put(readers.getReader(id),iterator);

java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/ReferenceGraph.java

@@ -6,6 +6,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.genotype.Variation;
 import net.sf.picard.reference.ReferenceSequence;
+import net.sf.picard.util.IntervalTree;
 import net.sf.samtools.util.StringUtil;
 
 import java.util.*;
@@ -14,8 +15,6 @@ import java.io.IOException;
 import java.io.ObjectOutputStream;
 import java.io.ObjectInputStream;
 
-import edu.mit.broad.picard.util.IntervalTree;
-
 /**
  * Created by IntelliJ IDEA.
  * User: depristo

java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java

@@ -22,9 +22,9 @@ import java.io.File;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.StringUtil;
 import net.sf.picard.reference.ReferenceSequence;
-import edu.mit.broad.picard.util.Interval;
+import net.sf.picard.util.Interval;
-import edu.mit.broad.picard.util.OverlapDetector;
+import net.sf.picard.util.OverlapDetector;
-import edu.mit.broad.picard.directed.IntervalList;
+import net.sf.picard.util.IntervalList;
 
 /**
  * Given intervals corresponding to targets or baits in a hybrid selection experiment, this walker gives the following interval-by-interval data:

java/src/org/broadinstitute/sting/playground/tools/vcf/GenotypeConcordance.java

@@ -4,9 +4,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
-import edu.mit.broad.picard.util.Interval;
-
-
 import java.io.*;
 import java.util.*;
 

java/src/org/broadinstitute/sting/playground/tools/vcf/VCFApplyCuts.java

@@ -7,7 +7,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
-import edu.mit.broad.picard.util.Interval;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;

java/src/org/broadinstitute/sting/playground/tools/vcf/VCFCallRates.java

@@ -4,13 +4,11 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
-import edu.mit.broad.picard.util.Interval;
-
-
 import java.io.*;
 import java.util.*;
 
 import net.sf.picard.PicardException;
+import net.sf.picard.util.Interval;
 import net.sf.picard.io.IoUtil;
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.ReferenceSequenceFile;

java/src/org/broadinstitute/sting/playground/tools/vcf/VCFHomogenizer.java

@@ -4,9 +4,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
             
 import org.broadinstitute.sting.utils.genotype.vcf.*;
         
-import edu.mit.broad.picard.util.Interval;
-
-
 import java.io.*;
 import java.util.*;
 import java.util.zip.*;

java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java

@@ -4,7 +4,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
-import edu.mit.broad.picard.util.Interval;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
@@ -14,6 +13,7 @@ import java.io.*;
 import java.util.*;
 
 import net.sf.picard.PicardException;
+import net.sf.picard.util.Interval;
 import net.sf.picard.io.IoUtil;
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.ReferenceSequenceFile;

java/src/org/broadinstitute/sting/playground/tools/vcf/VCFOptimize.java

@@ -4,7 +4,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
-import edu.mit.broad.picard.util.Interval;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;

java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis.java

@@ -4,13 +4,11 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
-import edu.mit.broad.picard.util.Interval;
-
-
 import java.io.*;
 import java.util.*;
 
 import net.sf.picard.PicardException;
+import net.sf.picard.util.Interval;
 import net.sf.picard.io.IoUtil;
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.ReferenceSequenceFile;

java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis2.java

@@ -4,14 +4,12 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
-import edu.mit.broad.picard.util.Interval;
-
-
 import java.io.*;
 import java.util.*;
 import java.lang.*;
 
 import net.sf.picard.PicardException;
+import net.sf.picard.util.Interval;
 import net.sf.picard.io.IoUtil;
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.ReferenceSequenceFile;

java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java

@@ -4,7 +4,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
-import edu.mit.broad.picard.util.Interval;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
@@ -14,6 +13,7 @@ import java.util.*;
 import java.util.zip.*;
 
 import net.sf.picard.PicardException;
+import net.sf.picard.util.Interval;
 import net.sf.picard.io.IoUtil;
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.ReferenceSequenceFile;

java/src/org/broadinstitute/sting/utils/GenomeLocParser.java

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.utils;
 
-import edu.mit.broad.picard.directed.IntervalList;
+import net.sf.picard.util.IntervalList;
-import edu.mit.broad.picard.util.Interval;
+import net.sf.picard.util.Interval;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;

java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java

@@ -341,5 +341,5 @@ public class GATKSAMRecord extends SAMRecord {
 
     public String toString() { return mRecord.toString(); }
 
-    public Chunk getCoordinates() { return mRecord.getCoordinates(); }
+    public BAMFileSpan getFilePointer() { return mRecord.getFilePointer(); }
 }

packages/PicardPrivate.xml

@@ -2,16 +2,12 @@
 <package name="picard-private-parts">
   <executable name="picard-private-parts">
     <dependencies>
-      <class name="edu.mit.broad.picard.directed.IntervalList" />
       <class name="edu.mit.broad.picard.genotype.DiploidGenotype" />
       <class name="edu.mit.broad.picard.genotype.geli.GeliFileReader" />
       <class name="edu.mit.broad.picard.genotype.geli.GeliFileWriter" />
       <class name="edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods" />
       <class name="edu.mit.broad.picard.util.BasicTextFileParser" />
       <class name="edu.mit.broad.picard.illumina.parser.IlluminaUtil" />
-      <class name="edu.mit.broad.picard.util.Interval" />
-      <class name="edu.mit.broad.picard.util.IntervalTree" />
-      <class name="edu.mit.broad.picard.util.OverlapDetector" />
       <class name="edu.mit.broad.picard.util.PasteParser" />
       <class name="edu.mit.broad.picard.variation.KnownVariantCodecV2" />
       <class name="edu.mit.broad.picard.variation.KnownVariantCodec" />

settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1333-sharding-4" status="integration" publication="20100324095800" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1333-sharding-5" status="integration" publication="20100326102100" />
 </ivy-module>

settings/repository/net.sf/picard-1.16.365-sharding.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.16.364-sharding" status="release" />
+    <info organisation="net.sf" module="picard" revision="1.16.365-sharding" status="release" />
 </ivy-module>

settings/repository/net.sf/sam-1.16.365-sharding.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.16.364-sharding" status="release" />
+    <info organisation="net.sf" module="sam" revision="1.16.365-sharding" status="release" />
 </ivy-module>