Major refactoring of shards. No longer uses interfaces but is now an actual object hierarchy with most of the important and common functionality pushed up to base classes. Eliminated a lot of duplicated code, and the shards are much more understandable now. Also now require a GenomeLocParser to work with their own GenomeLocs.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5030 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -3,11 +3,16 @@ package org.broadinstitute.sting.gatk.datasources.shards;
 import net.sf.samtools.*;
 import net.sf.picard.filter.SamRecordFilter;
 
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 
+import org.broadinstitute.sting.gatk.ReadProperties;
+import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 /**
  * A common interface for shards that natively understand the BAM format.
@@ -15,44 +20,90 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
  * @author mhanna
  * @version 0.1
  */
-public interface BAMFormatAwareShard extends Shard {
+public abstract class BAMFormatAwareShard extends Shard {
+    /**
+     * Whether the current location is unmapped.
+     */
+    private final boolean isUnmapped;
+
+    /**
+     * Reads data, if applicable.
+     */
+    private final SAMDataSource readsDataSource;
+
+    /**
+     * The data backing the next chunks to deliver to the traversal engine.
+     */
+    private final Map<SAMReaderID,SAMFileSpan> fileSpans;
+
+    public BAMFormatAwareShard(GenomeLocParser parser,
+                               ShardType shardType,
+                               List<GenomeLoc> locs,
+                               SAMDataSource readsDataSource,
+                               Map<SAMReaderID,SAMFileSpan> fileSpans,
+                               boolean isUnmapped) {
+        super(parser, shardType, locs);
+        this.readsDataSource = readsDataSource;
+        this.fileSpans = fileSpans;
+        this.isUnmapped = isUnmapped;
+    }
+
+    /**
+     * Closes the shard, tallying and incorporating read data.
+     */
+    @Override
+    public void close() {
+        readsDataSource.incorporateReadMetrics(readMetrics);
+    }
+
     /**
      * Get the list of chunks delimiting this shard.
      * @return a list of chunks that contain data for this shard.
      */
-    public Map<SAMReaderID,SAMFileSpan> getFileSpans();
+    public Map<SAMReaderID,SAMFileSpan> getFileSpans() {
+        return Collections.unmodifiableMap(fileSpans);
+    }
+
+    /**
+     * Gets key read validation and filtering properties.
+     * @return set of read properties associated with this shard.
+     */
+    @Override
+    public ReadProperties getReadProperties() {
+        return readsDataSource.getReadsInfo();
+    }
 
     /**
      * Returns true if this shard is meant to buffer reads, rather
      * than just holding pointers to their locations.
      * @return True if this shard can buffer reads.  False otherwise.
      */
-    public boolean buffersReads();
+    public boolean buffersReads() { return false; }
-
-    /**
-     * Checks to see whether the buffer is empty.
-     * @return True if the buffer is empty.
-     */
-    public boolean isBufferEmpty();
 
     /**
      * Returns true if the read buffer is currently full.
      * @return True if this shard's buffer is full (and the shard can buffer reads).
      */
-    public boolean isBufferFull();
+    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).
+     */
+    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.
      */
-    public void addRead(SAMRecord read);
+    public void addRead(SAMRecord read) { throw new UnsupportedOperationException("This shard does not buffer reads."); }
 
     /**
-     * Assuming this iterator buffers reads, an iterator to the reads
+     * Gets the iterator over the elements cached in the shard.
-     * stored in the shard.
+     * @return
-     * @return An iterator over the reads stored in the shard.
      */
-    public StingSAMIterator iterator();
+    public StingSAMIterator iterator() { throw new UnsupportedOperationException("This shard does not buffer reads."); }
+
 
     /**
      * Whether this shard points to an unmapped region.
@@ -60,5 +111,7 @@ public interface BAMFormatAwareShard extends Shard {
      * this case, isUnmapped should always return false.
      * @return True if this shard is unmapped.  False otherwise.
      */
-    public boolean isUnmapped();
+    public boolean isUnmapped() {
+        return isUnmapped;
+    }
 }

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

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
@@ -21,127 +22,14 @@ import net.sf.picard.filter.SamRecordFilter;
  * @version 1.0
  * @date Apr 7, 2009
  */
-public class LocusShard implements BAMFormatAwareShard {
+public class LocusShard extends BAMFormatAwareShard {
-    /**
-     * Source for read data.
-     */
-    private SAMDataSource dataSource;
-
-    /**
-     * A list of the chunks associated with this shard.
-     */
-    private final Map<SAMReaderID,SAMFileSpan> fileSpans;
-
-    // currently our location
-    private final List<GenomeLoc> loci;
-
-    /**
-     * Statistics about which reads in this shards were used and which were filtered away.
-     */
-    private final ReadMetrics readMetrics = new ReadMetrics();
-
     /**
      * Create a new locus shard, divided by index.
      * @param intervals List of intervals to process.
      * @param fileSpans File spans associated with that interval.
      */
-    public LocusShard(SAMDataSource dataSource, List<GenomeLoc> intervals, Map<SAMReaderID,SAMFileSpan> fileSpans) {
+    public LocusShard(GenomeLocParser parser, SAMDataSource dataSource, List<GenomeLoc> intervals, Map<SAMReaderID,SAMFileSpan> fileSpans) {
-        this.dataSource = dataSource;
+        super(parser, ShardType.LOCUS, intervals, dataSource, fileSpans, false);
-        this.loci = intervals;    
-        this.fileSpans = fileSpans;
-    }
-
-    /**
-     * Closes the shard, tallying and incorporating read data.
-     */
-    @Override
-    public void close() {
-        dataSource.incorporateReadMetrics(readMetrics);
-    }
-
-    /**
-     * Gets the file spans associated with this locus shard.
-     * @return A list of the file spans to use when retrieving locus data.
-     */
-    @Override
-    public Map<SAMReaderID,SAMFileSpan> getFileSpans() {
-        return fileSpans;
-    }
-
-    /** @return the genome location represented by this shard */
-    public List<GenomeLoc> getGenomeLocs() {
-        return loci;
-    }    
-
-    /**
-     * Returns true if this shard is meant to buffer reads, rather
-     * 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."); }
-
-    /**
-     * returns the type of shard.
-     */
-    @Override
-    public ShardType getShardType() {
-        return ShardType.LOCUS;
-    }
-
-    /**
-     * Locus shards don't make sense as unmapped regions.  Always return false.
-     * @return False always.
-     */
-    @Override
-    public boolean isUnmapped() {
-        return false;
-    }
-
-    /**
-     * Gets key read validation and filtering properties.
-     * @return set of read properties associated with this shard.
-     */
-    @Override
-    public ReadProperties getReadProperties() {
-        return dataSource.getReadsInfo();
-    }
-
-    /**
-     * Retrieves a storage space of metrics about number of reads included, filtered, etc.
-     * @return Storage space for metrics.
-     */    
-    @Override
-    public ReadMetrics getReadMetrics() {
-        return readMetrics;
     }
 
     /**
@@ -150,6 +38,6 @@ public class LocusShard implements BAMFormatAwareShard {
      */
     @Override
     public String toString() {
-        return Utils.join(";",loci);
+        return Utils.join(";",getGenomeLocs());
     }
 }

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

@@ -48,6 +48,11 @@ public class LocusShardStrategy implements ShardStrategy {
      */
     private final SAMDataSource reads;
 
+    /**
+     * the parser for creating shards
+     */
+    private GenomeLocParser genomeLocParser;
+
     /**
      * An iterator through the available file pointers.
      */
@@ -60,6 +65,8 @@ public class LocusShardStrategy implements ShardStrategy {
      */
     LocusShardStrategy(SAMDataSource reads, IndexedFastaSequenceFile reference, GenomeLocParser genomeLocParser, GenomeLocSortedSet locations) {
         this.reads = reads;
+        this.genomeLocParser = genomeLocParser;
+
         if(!reads.isEmpty()) {
             GenomeLocSortedSet intervals;
             if(locations == null) {
@@ -124,7 +131,7 @@ public class LocusShardStrategy implements ShardStrategy {
     public LocusShard next() {
         FilePointer nextFilePointer = filePointerIterator.next();
         Map<SAMReaderID,SAMFileSpan> fileSpansBounding = nextFilePointer.fileSpans != null ? nextFilePointer.fileSpans : null;
-        return new LocusShard(reads,nextFilePointer.locations,fileSpansBounding);
+        return new LocusShard(genomeLocParser, reads,nextFilePointer.locations,fileSpansBounding);
     }
 
     /** we don't support the remove command */

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.gatk.ReadMetrics;
@@ -13,81 +14,16 @@ import java.util.List;
  * @author mhanna
  * @version 0.1
  */
-public class MonolithicShard implements Shard {
+public class MonolithicShard extends BAMFormatAwareShard {
-    /**
-     * Reads data, if applicable.
-     */
-    private final SAMDataSource readsDataSource;
-
-    /**
-     * What type of MonolithicShard is this?  Read or locus?
-     */
-    private final ShardType shardType;
-
-    /**
-     * Locations.  For the monolithic shard, should be a list of all available contigs in the reference.
-     */
-    private final List<GenomeLoc> locs;
-
-    /**
-     * Statistics about which reads in this shards were used and which were filtered away.
-     */
-    private final ReadMetrics readMetrics = new ReadMetrics();
-
     /**
      * Creates a new monolithic shard of the given type.
      * @param shardType Type of the shard.  Must be either read or locus; cannot be intervalic.
      * @param locs Intervals that this monolithic shard should process. 
      */
-    public MonolithicShard(SAMDataSource readsDataSource, ShardType shardType, List<GenomeLoc> locs) {
+    public MonolithicShard(GenomeLocParser parser, SAMDataSource readsDataSource, ShardType shardType, List<GenomeLoc> locs) {
-        this.readsDataSource = readsDataSource;
+        super(parser, shardType, locs, readsDataSource, null, false);
         if(shardType != ShardType.LOCUS && shardType != ShardType.READ)
             throw new ReviewedStingException("Invalid shard type for monolithic shard: " + shardType);
-        this.shardType = shardType;
-        this.locs = locs;
-    }
-
-    /**
-     * Closes the shard, tallying and incorporating read data.
-     */
-    @Override
-    public void close() {
-        readsDataSource.incorporateReadMetrics(readMetrics);
-    }
-
-    /**
-     * Returns null, indicating that (in this case) the entire genome is covered.
-     * @return null.
-     */
-    public List<GenomeLoc> getGenomeLocs() {
-        return locs;
-    }
-
-    /**
-     * Reports the type of monolithic shard.
-     * @return Type of monolithic shard.
-     */
-    @Override
-    public ShardType getShardType() {
-        return shardType;
-    }
-
-    /**
-     * Gets key read validation and filtering properties.
-     * @return set of read properties associated with this shard.
-     */
-    @Override
-    public ReadProperties getReadProperties() {
-        return readsDataSource.getReadsInfo();
-    }
-
-    /**
-     * Retrieves a storage space of metrics about number of reads included, filtered, etc.
-     * @return Storage space for metrics.
-     */
-    @Override
-    public ReadMetrics getReadMetrics() {
-        return readMetrics;
     }
 
     /**

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

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Iterator;
 import java.util.NoSuchElementException;
@@ -23,8 +24,8 @@ public class MonolithicShardStrategy implements ShardStrategy {
      * Create a new shard strategy for shards of the given type.
      * @param shardType The shard type.
      */
-    public MonolithicShardStrategy(final SAMDataSource readsDataSource, final Shard.ShardType shardType, final List<GenomeLoc> region) {
+    public MonolithicShardStrategy(final GenomeLocParser parser, final SAMDataSource readsDataSource, final Shard.ShardType shardType, final List<GenomeLoc> region) {
-        shard = new MonolithicShard(readsDataSource,shardType,region);
+        shard = new MonolithicShard(parser,readsDataSource,shardType,region);
     }
 
     /**

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

@@ -13,6 +13,7 @@ import java.util.*;
 import net.sf.samtools.SAMFileSpan;
 import net.sf.samtools.SAMRecord;
 import net.sf.picard.filter.SamRecordFilter;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 /**
  *
@@ -36,80 +37,21 @@ import net.sf.picard.filter.SamRecordFilter;
  * @author mhanna
  * @version 0.1
  */
-public class ReadShard implements BAMFormatAwareShard {
+public class ReadShard extends BAMFormatAwareShard {
-    private final SAMDataSource readsDataSource;
-
-    /**
-     * The data backing the next chunks to deliver to the traversal engine.
-     */
-    private final Map<SAMReaderID,SAMFileSpan> fileSpans;
-
     /**
      * The reads making up this shard.
      */
     private final Collection<SAMRecord> reads = new ArrayList<SAMRecord>(ReadShardStrategy.MAX_READS);
 
-    /**
+    public ReadShard(GenomeLocParser parser, SAMDataSource readsDataSource, Map<SAMReaderID,SAMFileSpan> fileSpans, List<GenomeLoc> loci, boolean isUnmapped) {
-     * currently our location
+        super(parser, ShardType.READ, loci, readsDataSource, fileSpans, isUnmapped);
-     */
-    private final List<GenomeLoc> loci;
-
-    /**
-     * Whether the current location is unmapped.
-     */
-    private final boolean isUnmapped;
-
-    /**
-     * Statistics about which reads in this shards were used and which were filtered away.
-     */
-    private final ReadMetrics readMetrics = new ReadMetrics();
-
-    public ReadShard(SAMDataSource readsDataSource, Map<SAMReaderID,SAMFileSpan> fileSpans, List<GenomeLoc> loci, boolean isUnmapped) {
-        this.readsDataSource = readsDataSource;
-        this.fileSpans = fileSpans;
-        this.loci = loci;
-        this.isUnmapped = isUnmapped;
     }
 
-    /**
-     * Closes the shard, tallying and incorporating read data.
-     */
-    @Override
-    public void close() {
-        readsDataSource.incorporateReadMetrics(readMetrics);
-    }    
-
-    /**
-     * Get the list of chunks delimiting this shard.
-     * @return a list of chunks that contain data for this shard.
-     */
-    @Override
-    public Map<SAMReaderID,SAMFileSpan> getFileSpans() {
-        return Collections.unmodifiableMap(fileSpans);
-    }
-
-    /** @return the genome location represented by this shard */
-    @Override
-    public List<GenomeLoc> getGenomeLocs() {
-        return loci;
-    }
-
-    /**
-     * Whether this shard points to an unmapped region.
-     * @return True if this shard is unmapped.  False otherwise.
-     */
-    @Override
-    public boolean isUnmapped() {
-        return isUnmapped;
-    }
-
-
     /**
      * Returns true if this shard is meant to buffer reads, rather
      * than just holding pointers to their locations.
      * @return True if this shard can buffer reads.  False otherwise.
      */
-    @Override
     public boolean buffersReads() {
         return true;
     }
@@ -118,7 +60,6 @@ public class ReadShard implements BAMFormatAwareShard {
      * 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;
     }
@@ -127,7 +68,6 @@ public class ReadShard implements BAMFormatAwareShard {
      * 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() > ReadShardStrategy.MAX_READS;
     }
@@ -136,7 +76,6 @@ public class ReadShard implements BAMFormatAwareShard {
      * 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.
@@ -147,39 +86,10 @@ public class ReadShard implements BAMFormatAwareShard {
      * Creates an iterator over reads stored in this shard's read cache.
      * @return
      */
-    @Override
     public StingSAMIterator iterator() {
         return StingSAMIteratorAdapter.adapt(reads.iterator());
     }
 
-    /**
-     * what kind of shard do we return
-     *
-     * @return ShardType, indicating the type
-     */
-    @Override
-    public ShardType getShardType() {
-        return ShardType.READ;
-    }
-
-    /**
-     * Gets key read validation and filtering properties.
-     * @return set of read properties associated with this shard.
-     */
-    @Override
-    public ReadProperties getReadProperties() {
-        return readsDataSource.getReadsInfo();
-    }
-
-    /**
-     * Retrieves a storage space of metrics about number of reads included, filtered, etc.
-     * @return Storage space for metrics.
-     */    
-    @Override
-    public ReadMetrics getReadMetrics() {
-        return readMetrics;
-    }
-
     /**
      * String representation of this shard.
      * @return A string representation of the boundaries of this shard.
@@ -187,7 +97,7 @@ public class ReadShard implements BAMFormatAwareShard {
     @Override
     public String toString() {
         StringBuilder sb = new StringBuilder();
-        for(Map.Entry<SAMReaderID,SAMFileSpan> entry: fileSpans.entrySet()) {
+        for(Map.Entry<SAMReaderID,SAMFileSpan> entry: getFileSpans().entrySet()) {
             sb.append(entry.getKey());
             sb.append(": ");
             sb.append(entry.getValue());
@@ -195,6 +105,4 @@ public class ReadShard implements BAMFormatAwareShard {
         }
         return sb.toString();
     }
-
-
 }

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

@@ -31,6 +31,7 @@ import java.util.*;
 
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 
 /**
@@ -84,13 +85,16 @@ public class ReadShardStrategy implements ShardStrategy {
      */
     private boolean isIntoUnmappedRegion = false;
 
+    private final GenomeLocParser parser;
+
     /**
      * Create a new read shard strategy, loading read shards from the given BAM file.
      * @param dataSource Data source from which to load shards.
      * @param locations intervals to use for sharding.
      */
-    public ReadShardStrategy(SAMDataSource dataSource, GenomeLocSortedSet locations) {
+    public ReadShardStrategy(GenomeLocParser parser, SAMDataSource dataSource, GenomeLocSortedSet locations) {
         this.dataSource = dataSource;
+        this.parser = parser;
         this.position = this.dataSource.getCurrentPosition();
         this.locations = locations;
 
@@ -155,7 +159,7 @@ public class ReadShardStrategy implements ShardStrategy {
                 }
 
                 if(selectedReaders.size() > 0) {
-                    BAMFormatAwareShard shard = new ReadShard(dataSource,selectedReaders,currentFilePointer.locations,currentFilePointer.isRegionUnmapped);
+                    BAMFormatAwareShard shard = new ReadShard(parser, dataSource,selectedReaders,currentFilePointer.locations,currentFilePointer.isRegionUnmapped);
                     dataSource.fillShard(shard);
 
                     if(!shard.isBufferEmpty()) {
@@ -169,7 +173,9 @@ public class ReadShardStrategy implements ShardStrategy {
             }
         }
         else {
-            BAMFormatAwareShard shard = new ReadShard(dataSource,position,null,false);
+            // todo -- this nulling of intervals is a bit annoying since readwalkers without
+            // todo -- any -L values need to be special cased throughout the code.
+            BAMFormatAwareShard shard = new ReadShard(parser,dataSource,position,null,false);
             dataSource.fillShard(shard);
             nextShard = !shard.isBufferEmpty() ? shard : null;
         }

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

@@ -3,6 +3,9 @@ package org.broadinstitute.sting.gatk.datasources.shards;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.gatk.ReadProperties;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.HasGenomeLocation;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.Serializable;
 import java.util.List;
@@ -29,41 +32,101 @@ import java.util.List;
  * <p/>
  * Interface Shard
  * <p/>
- * The base interface for shards.
+ * The base abstract class for shards.
  */
-public interface Shard extends Serializable {
+public abstract class Shard implements HasGenomeLocation {
-    enum ShardType {
+    public enum ShardType {
         READ, LOCUS
     }
 
+    protected final GenomeLocParser parser; // incredibly annoying!
+
+    /**
+     * What type of MonolithicShard is this?  Read or locus?
+     */
+    protected final ShardType shardType;
+
+    /**
+     * Locations.  For the monolithic shard, should be a list of all available contigs in the reference.
+     */
+    protected final List<GenomeLoc> locs;
+
+    /**
+     * Statistics about which reads in this shards were used and which were filtered away.
+     */
+    protected final ReadMetrics readMetrics = new ReadMetrics();
+
+    public Shard(GenomeLocParser parser, ShardType shardType, List<GenomeLoc> locs) {
+        this.locs = locs;
+        this.parser = parser;
+        this.shardType = shardType;
+    }
+
     /**
      * If isUnmapped is true, than getGenomeLocs by
      * definition will return a singleton list with a GenomeLoc.UNMAPPED
      *
+     * Can return null, indicating that the entire genome is covered.
+     *
      * @return the genome location represented by this shard
      */
-    public List<GenomeLoc> getGenomeLocs();
+    public List<GenomeLoc> getGenomeLocs() {
+        return locs;
+    }
+
+    /**
+     * Returns the span of the genomeLocs comprising this shard
+     * @param
+     * @return
+     */
+    public GenomeLoc getLocation() {
+        if ( getGenomeLocs() == null )
+            return GenomeLoc.WHOLE_GENOME;
+
+        int start = Integer.MAX_VALUE;
+        int stop = Integer.MIN_VALUE;
+        String contig = null;
+
+        for ( GenomeLoc loc : getGenomeLocs() ) {
+            if ( GenomeLoc.isUnmapped(loc) )
+                // special case the unmapped region marker, just abort out
+                return loc;
+            contig = loc.getContig();
+            if ( loc.getStart() < start ) start = loc.getStart();
+            if ( loc.getStop() > stop ) stop = loc.getStop();
+        }
+
+        return parser.createGenomeLoc(contig, start, stop);
+    }
+
 
     /**
      * what kind of shard do we return
      * @return ShardType, indicating the type
      */
-    public ShardType getShardType();
+    public ShardType getShardType() {
+        return shardType;
+    }
 
     /**
      * Does any releasing / aggregation required when the shard is through being processed.
      */
-    public void close();
+    public void close() {
+        ; // by default don't do anything
+    }
 
     /**
      * Gets required configuration for validating and filtering reads.
      * @return read configuration properties.
      */
-    public ReadProperties getReadProperties();
+    public abstract ReadProperties getReadProperties();
 
     /**
      * Gets the runtime metrics associated with this shard.
-     * @return metrics and read counts.
+     * Retrieves a storage space of metrics about number of reads included, filtered, etc.
+     * @return Storage space for metrics.
      */
-    public ReadMetrics getReadMetrics();
+    public ReadMetrics getReadMetrics() {
+        return readMetrics;
+    }
 }

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

@@ -70,7 +70,7 @@ public class ShardStrategyFactory {
             case LOCUS_EXPERIMENTAL:
                 return new LocusShardStrategy(readsDataSource,referenceDataSource,genomeLocParser,null);
             case READS_EXPERIMENTAL:
-                return new ReadShardStrategy(readsDataSource,null);
+                return new ReadShardStrategy(genomeLocParser,readsDataSource,null);
             default:
                 throw new ReviewedStingException("Strategy: " + strat + " isn't implemented for this type of shatter request");
         }
@@ -108,7 +108,7 @@ public class ShardStrategyFactory {
             case LOCUS_EXPERIMENTAL:
                 return new LocusShardStrategy(readsDataSource,referenceDataSource,genomeLocParser,lst);
             case READS_EXPERIMENTAL:
-                return new ReadShardStrategy(readsDataSource,lst);
+                return new ReadShardStrategy(genomeLocParser, readsDataSource,lst);
             default:
                 throw new ReviewedStingException("Strategy: " + strat + " isn't implemented");
         }