Cleaning up the inheritance hierarchy from the previous commit.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2738 348d0f76-0448-11de-a6fe-93d51630548a

java/src/net/sf/samtools/BAMFileReader2.java

@@ -41,7 +41,7 @@ import java.net.URL;
  * Internal class for reading and querying BAM files.
  */
 class BAMFileReader2
-    extends SAMFileReader2.ReaderImplementation2 {
+    extends SAMFileReader.ReaderImplementation {
     // True if reading from a File rather than an InputStream
     private boolean mIsSeekable = false;
     // For converting bytes into other primitive types

java/src/net/sf/samtools/SAMFileReader2.java

@@ -62,14 +62,6 @@ public class SAMFileReader2 implements Iterable<SAMRecord> {
     private ReaderImplementation mReader = null;
     private File samFile = null;
 
-    /**
-     * Internal interface for SAM/BAM file reader implementations.
-     * Implemented as an abstract class to enforce better access control.
-     */
-    static abstract class ReaderImplementation2 extends SAMFileReader.ReaderImplementation {
-        abstract CloseableIterator<SAMRecord> getIterator(List<Chunk> chunks);
-    }
-
     /**
      * Prepare to read a SAM or BAM file.  Indexed lookup not allowed because reading from InputStream.
      */
@@ -200,14 +192,14 @@ public class SAMFileReader2 implements Iterable<SAMRecord> {
     public CloseableIterator<SAMRecord> iterator(List<Chunk> chunks) {
         // TODO: Add sanity checks so that we're not doing this against a BAM file.
         if(!(mReader instanceof BAMFileReader2))
-            throw new PicardException("This call requires a ReaderImplementation2-compliant interface");
+            throw new PicardException("This call cannot be performed without a backing BAMFileReader2");
         return ((BAMFileReader2)mReader).getIterator(chunks);
     }
 
     public List<Chunk> getOverlappingFilePointers(final String sequence, final int start, final int end) {
         // TODO: Add sanity checks so that we're not doing this against a BAM file.
         if(!(mReader instanceof BAMFileReader2))
-            throw new PicardException("This call requires a ReaderImplementation2-compliant interface");
+            throw new PicardException("This call cannot be performed without a backing BAMFileReader2");
         return ((BAMFileReader2)mReader).getOverlappingFilePointers(sequence,start,end);
     }
 

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

@@ -0,0 +1,19 @@
+package org.broadinstitute.sting.gatk.datasources.shards;
+
+import net.sf.samtools.Chunk;
+
+import java.util.List;
+
+/**
+ * A common interface for shards that natively understand the BAM format.
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+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 List<Chunk> getChunks();    
+}

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

@@ -10,7 +10,7 @@ import java.util.List;
  * @author mhanna
  * @version 0.1
  */
-public class BlockDelimitedReadShard extends ReadShard {
+public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAwareShard {
     /**
      * The list of chunks to retrieve when loading this shard.
      */

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

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.Chunk;
 
 import java.util.List;
@@ -35,29 +36,30 @@ import java.util.List;
 /**
  * A shard that's delimited based on the index rather than
  */
-public class IndexDelimitedLocusShard implements Shard {
+public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwareShard {
-
-    /**
-     * a collection of genomic locations to interate over
-     */
-    private final GenomeLocSortedSet intervals;
-
     /**
      * A list of the chunks associated with this shard.
      */
     private final List<Chunk> chunks;
 
-    IndexDelimitedLocusShard(GenomeLocSortedSet intervals, List<Chunk> chunks) {
+    /**
-        this.intervals = intervals;
+     * An IndexDelimitedLocusShard can be used either for LOCUS or LOCUS_INTERVAL shard types.
-        this.chunks = chunks;
+     * Track which type is being used.
-    }
+     */
+    private final ShardType shardType;
 
     /**
-     * The locations represented by this shard.
+     * Create a new locus shard, divided by index.
-     * @return the genome location represented by this shard
+     * @param intervals List of intervals to process.
+     * @param chunks Chunks associated with that interval.
+     * @param shardType Type of the shard; must be either LOCUS or LOCUS_INTERVAL.
      */
-    public List<GenomeLoc> getGenomeLocs() {
+    IndexDelimitedLocusShard(List<GenomeLoc> intervals, List<Chunk> chunks, ShardType shardType) {
-        return intervals.toList();
+        super(intervals);
+        this.chunks = chunks;
+        if(shardType != ShardType.LOCUS && shardType != ShardType.LOCUS_INTERVAL)
+            throw new StingException("Attempted to create an IndexDelimitedLocusShard with invalid shard type: " + shardType);
+        this.shardType = shardType;
     }
 
     /**
@@ -69,19 +71,10 @@ public class IndexDelimitedLocusShard implements Shard {
     }
 
     /**
-     * returns the type of shard, LOCUS_INTERVAL.
+     * returns the type of shard.
-     * @return LOCUS_INTERVAL, indicating the shard type
-     */
-    public ShardType getShardType() {
-        return ShardType.LOCUS_INTERVAL;
-    }
-
-    /**
-     * String representation of this shard.
-     * @return A string representation of the boundaries of this shard.
      */
     @Override
-    public String toString() {
+    public ShardType getShardType() {
-        return intervals.toString();
+        return shardType;
     }
 }

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

@@ -78,7 +78,7 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
         List<Chunk> filePointers = locations.get(loc);
         locations.remove(loc);
         
-        return new IndexDelimitedLocusShard(GenomeLocSortedSet.createSetFromList(Arrays.asList(loc)),filePointers); 
+        return new IndexDelimitedLocusShard(Collections.singletonList(loc),filePointers,Shard.ShardType.LOCUS_INTERVAL); 
     }
 
     /** we don't support the remove command */

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.Utils;
 
 import java.util.Collections;
 import java.util.List;
@@ -34,17 +35,16 @@ import java.util.List;
  * in place so it's easier to change guts later.
  */
 public class LocusShard implements Shard {
-
     // currently our location
-    final GenomeLoc mLoc;
+    final List<GenomeLoc> loci;
 
-    public LocusShard(GenomeLoc loc) {
+    public LocusShard(List<GenomeLoc> loci) {
-        this.mLoc = loc;
+        this.loci = loci;
     }
 
     /** @return the genome location represented by this shard */
     public List<GenomeLoc> getGenomeLocs() {
-        return Collections.singletonList(mLoc);
+        return loci;
     }
 
     /**
@@ -56,21 +56,12 @@ public class LocusShard implements Shard {
         return ShardType.LOCUS;
     }
 
-    /**
-     * return a shard representing the passed in GenomeLoc
-     *
-     * @return
-     */
-    public static LocusShard toShard(GenomeLoc loc) {
-        return new LocusShard(loc);
-    }
-
     /**
      * String representation of this shard.
      * @return A string representation of the boundaries of this shard.
      */
     @Override
     public String toString() {
-        return mLoc.toString();
+        return Utils.join(";",loci);
     }
 }

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

@@ -8,6 +8,7 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Iterator;
+import java.util.Collections;
 /**
  *
  * User: aaron
@@ -195,7 +196,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
         if (nextStart + proposedSize - 1 < length) {
             lastGenomeLocSize = proposedSize;
             mLoc = GenomeLocParser.createGenomeLoc(dic.getSequence(seqLoc).getSequenceIndex(), nextStart, nextStart + proposedSize - 1);
-            return LocusShard.toShard(mLoc);
+            return new LocusShard(Collections.singletonList(mLoc));
         }
         // else we can't make it in the current location, we have to stitch one together
         else {
@@ -208,7 +209,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
 
             // move to the next contig
             // the next sequence should start at the begining of the next contig
-            Shard ret = LocusShard.toShard(GenomeLocParser.createGenomeLoc(dic.getSequence(seqLoc).getSequenceIndex(), nextStart, nextStart + lastGenomeLocSize - 1));
+            Shard ret = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc(dic.getSequence(seqLoc).getSequenceIndex(), nextStart, nextStart + lastGenomeLocSize - 1)));
 
             // now  jump ahead to the next contig
             jumpContig();

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

@@ -49,27 +49,19 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
     }
 
     public StingSAMIterator seek(Shard shard) {
-        if(!(shard instanceof BlockDelimitedReadShard) && !(shard instanceof IndexDelimitedLocusShard))
+        if(!(shard instanceof BAMFormatAwareShard))
-            throw new StingException("BlockDrivenSAMDataSource cannot operate on shards of type: " + shard);
+            throw new StingException("BlockDrivenSAMDataSource cannot operate on shards of type: " + shard.getClass());
 
-        if(shard instanceof ReadShard) {
+        // Since the beginning of time for the GATK, enableVerification has been true only for ReadShards.  I don't
-            CloseableIterator<SAMRecord> iterator = reader.iterator(((BlockDelimitedReadShard)shard).getChunks());
+        // know why this is.  Please add a comment here if you do.
-            return applyDecoratingIterators(true,
+        boolean enableVerification = shard instanceof ReadShard;
-                    StingSAMIteratorAdapter.adapt(reads, iterator),
-                    reads.getDownsamplingFraction(),
-                    reads.getValidationExclusionList().contains(ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION),
-                    reads.getSupplementalFilters());
-        }
-        else if(shard instanceof IndexDelimitedLocusShard) {
-            CloseableIterator<SAMRecord> iterator = reader.iterator(((IndexDelimitedLocusShard)shard).getChunks());
-            return applyDecoratingIterators(false,
-                    StingSAMIteratorAdapter.adapt(reads, iterator),
-                    reads.getDownsamplingFraction(),
-                    reads.getValidationExclusionList().contains(ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION),
-                    reads.getSupplementalFilters());
-        }
 
-        throw new UnsupportedOperationException("Unable to infer type of this shard.");
+        CloseableIterator<SAMRecord> iterator = reader.iterator(((BAMFormatAwareShard)shard).getChunks());
+        return applyDecoratingIterators(enableVerification,
+                StingSAMIteratorAdapter.adapt(reads,iterator),
+                reads.getDownsamplingFraction(),
+                reads.getValidationExclusionList().contains(ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION),
+                reads.getSupplementalFilters());
     }
 
     /**

java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java

@@ -11,6 +11,8 @@ import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
 
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.samtools.util.StringUtil;
+
+import java.util.Collections;
 /*
  * Copyright (c) 2009 The Broad Institute
  *
@@ -54,7 +56,7 @@ public class LocusReferenceViewTest extends ReferenceViewTemplate {
 
     @Test
     public void testOverlappingReferenceBases() {
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length()));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc(0, sequenceFile.getSequence("chrM").length() - 10, sequenceFile.getSequence("chrM").length())));
 
         ShardDataProvider dataProvider = new ShardDataProvider(shard, null, sequenceFile, null);
         LocusReferenceView view = new LocusReferenceView(dataProvider);
@@ -71,7 +73,7 @@ public class LocusReferenceViewTest extends ReferenceViewTemplate {
     /** Queries outside the bounds of the shard should generate an error. */
     @Test(expected = InvalidPositionException.class)
     public void testBoundsFailure() {
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc(0, 1, 50));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc(0, 1, 50)));
 
         ShardDataProvider dataProvider = new ShardDataProvider(shard, null, sequenceFile, null);
         LocusReferenceView view = new LocusReferenceView(dataProvider);
@@ -86,7 +88,7 @@ public class LocusReferenceViewTest extends ReferenceViewTemplate {
      * @param loc
      */
     protected void validateLocation( GenomeLoc loc ) {
-        Shard shard = new LocusShard(loc);
+        Shard shard = new LocusShard(Collections.singletonList(loc));
         GenomeLocusIterator shardIterator = new GenomeLocusIterator(shard.getGenomeLocs());
 
         ShardDataProvider dataProvider = new ShardDataProvider(shard, null, sequenceFile, null);

java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java

@@ -45,7 +45,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator();
 
         GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1", 1, 5);
-        Shard shard = new LocusShard(shardBounds);
+        Shard shard = new LocusShard(Collections.singletonList(shardBounds));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
 
         LocusView view = createView(dataProvider);
@@ -59,7 +59,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1", 1, 5);
-        Shard shard = new LocusShard(shardBounds);
+        Shard shard = new LocusShard(Collections.singletonList(shardBounds));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
 
         LocusView view = createView(dataProvider);
@@ -72,7 +72,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read = buildSAMRecord("chr1", 1, 5);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
         LocusView view = createView(dataProvider);
 
@@ -84,7 +84,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read = buildSAMRecord("chr1", 6, 10);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
         LocusView view = createView(dataProvider);
 
@@ -96,7 +96,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read = buildSAMRecord("chr1", 3, 7);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
         LocusView view = createView(dataProvider);
 
@@ -108,7 +108,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read = buildSAMRecord("chr1", 1, 10);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 6, 15));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 6, 15)));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
         LocusView view = createView(dataProvider);
 
@@ -120,7 +120,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read = buildSAMRecord("chr1", 6, 15);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
         LocusView view = createView(dataProvider);
 
@@ -133,7 +133,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read2 = buildSAMRecord("chr1", 6, 10);
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2);
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
         LocusView view = createView(dataProvider);
 
@@ -150,7 +150,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read4 = buildSAMRecord("chr1", 6, 10);
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
         LocusView view = createView(dataProvider);
 
@@ -167,7 +167,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read4 = buildSAMRecord("chr1", 5, 9);
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
         LocusView view = createView(dataProvider);
 
@@ -186,7 +186,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read6 = buildSAMRecord("chr1", 6, 10);
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4, read5, read6);
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 1, 10)));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
         LocusView view = createView(dataProvider);
 
@@ -212,7 +212,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read01, read02, read03, read04, read05, read06,
                                                            read07, read08, read09, read10, read11, read12);
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 6, 15));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chr1", 6, 15)));
         ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
         LocusView view = createView(dataProvider);
 

java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewTest.java

@@ -52,7 +52,7 @@ public class ReferenceOrderedViewTest extends BaseTest {
      */
     @Test
     public void testNoBindings() {
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chrM",1,30));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chrM",1,30)));
         ShardDataProvider provider = new ShardDataProvider(shard, null, seq, Collections.<ReferenceOrderedDataSource>emptyList());
         ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
 
@@ -69,7 +69,7 @@ public class ReferenceOrderedViewTest extends BaseTest {
         ReferenceOrderedData rod = new ReferenceOrderedData("tableTest", file, TabularROD.class);
         ReferenceOrderedDataSource dataSource = new ReferenceOrderedDataSource(rod);
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chrM",1,30));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chrM",1,30)));
 
         ShardDataProvider provider = new ShardDataProvider(shard, null, seq, Collections.singletonList(dataSource));
         ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
@@ -95,7 +95,7 @@ public class ReferenceOrderedViewTest extends BaseTest {
         ReferenceOrderedDataSource dataSource2 = new ReferenceOrderedDataSource(rod2);
 
 
-        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chrM",1,30));
+        Shard shard = new LocusShard(Collections.singletonList(GenomeLocParser.createGenomeLoc("chrM",1,30)));
 
         ShardDataProvider provider = new ShardDataProvider(shard, null, seq, Arrays.asList(dataSource1,dataSource2));
         ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );