Made IntervalSharder respect the IntervalMergingRule specified on the command line

* This addresses PT Bug 69741902
* Added a required IMR argument to FilePointer, BAMScheduler, IntervalSharder, and SAMDataSource
* This rule is used by FilePointer.combine and FilePointer.union
* Added unit and integration tests

public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -888,7 +888,8 @@ public class GenomeAnalysisEngine {
                 argCollection.defaultBaseQualities,
                 removeProgramRecords,
                 keepReadsInLIBS,
-                sampleRenameMap);
+                sampleRenameMap,
+                argCollection.intervalArguments.intervalMerging);
     }
 
     /**

public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java

@@ -34,6 +34,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.*;
@@ -51,6 +52,7 @@ public class BAMScheduler implements Iterator<FilePointer> {
     private GenomeLocSortedSet loci;
     private PeekableIterator<GenomeLoc> locusIterator;
     private GenomeLoc currentLocus;
+    private IntervalMergingRule intervalMergingRule;
 
     /*
      * Creates BAMScheduler using contigs from the given BAM data source.
@@ -59,27 +61,28 @@ public class BAMScheduler implements Iterator<FilePointer> {
      * @return non-null BAM scheduler
      */
     public static BAMScheduler createOverMappedReads(final SAMDataSource dataSource) {
-        final BAMScheduler scheduler = new BAMScheduler(dataSource);
+        final BAMScheduler scheduler = new BAMScheduler(dataSource, IntervalMergingRule.ALL);
         final GenomeLocSortedSet intervals = GenomeLocSortedSet.createSetFromSequenceDictionary(dataSource.getHeader().getSequenceDictionary());
         scheduler.populateFilteredIntervalList(intervals);
         return scheduler;
     }
 
     public static BAMScheduler createOverAllReads(final SAMDataSource dataSource, final GenomeLocParser parser) {
-        BAMScheduler scheduler = new BAMScheduler(dataSource);
+        BAMScheduler scheduler = new BAMScheduler(dataSource, IntervalMergingRule.ALL);
         scheduler.populateUnfilteredIntervalList(parser);
         return scheduler;
     }
 
-    public static BAMScheduler createOverIntervals(final SAMDataSource dataSource, final GenomeLocSortedSet loci) {
+    public static BAMScheduler createOverIntervals(final SAMDataSource dataSource, final IntervalMergingRule mergeRule, final GenomeLocSortedSet loci) {
-        BAMScheduler scheduler = new BAMScheduler(dataSource);
+        BAMScheduler scheduler = new BAMScheduler(dataSource, mergeRule);
         scheduler.populateFilteredIntervalList(loci);
         return scheduler;
     }
 
 
-    private BAMScheduler(final SAMDataSource dataSource) {
+    private BAMScheduler(final SAMDataSource dataSource, final IntervalMergingRule mergeRule) {
         this.dataSource = dataSource;
+        this.intervalMergingRule = mergeRule;
         for(SAMReaderID reader: dataSource.getReaderIDs()) {
             GATKBAMIndex index = dataSource.getIndex(reader);
             if(index != null)
@@ -124,7 +127,7 @@ public class BAMScheduler implements Iterator<FilePointer> {
      * @return A file pointer over the specified region.
      */
     private FilePointer generatePointerOverEntireFileset() {
-        FilePointer filePointer = new FilePointer();
+        FilePointer filePointer = new FilePointer(intervalMergingRule);
 
         // This is a "monolithic" FilePointer representing all regions in all files we will ever visit, and is
         // the only FilePointer we will create. This allows us to have this FilePointer represent regions from
@@ -165,14 +168,14 @@ public class BAMScheduler implements Iterator<FilePointer> {
         while(nextFilePointer == null && currentLocus != null) {
             // special case handling of the unmapped shard.
             if(currentLocus == GenomeLoc.UNMAPPED) {
-                nextFilePointer = new FilePointer(GenomeLoc.UNMAPPED);
+                nextFilePointer = new FilePointer(intervalMergingRule, GenomeLoc.UNMAPPED);
                 for(SAMReaderID id: dataSource.getReaderIDs())
                     nextFilePointer.addFileSpans(id,createSpanToEndOfFile(indexFiles.get(id).getStartOfLastLinearBin()));
                 currentLocus = null;
                 continue;
             }
 
-            nextFilePointer = new FilePointer();
+            nextFilePointer = new FilePointer(intervalMergingRule);
 
             int coveredRegionStart = 1;
             int coveredRegionStop = Integer.MAX_VALUE;

public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java

@@ -45,6 +45,7 @@ import java.util.*;
 public class FilePointer {
     protected final SortedMap<SAMReaderID,SAMFileSpan> fileSpans = new TreeMap<SAMReaderID,SAMFileSpan>();
     protected final List<GenomeLoc> locations = new ArrayList<GenomeLoc>();
+    protected final IntervalMergingRule intervalMergingRule;
 
     /**
      * Does this file pointer point into an unmapped region?
@@ -65,7 +66,8 @@ public class FilePointer {
     private Integer contigIndex = null;
 
 
-    public FilePointer( List<GenomeLoc> locations ) {
+    public FilePointer( final IntervalMergingRule mergeRule, final List<GenomeLoc> locations ) {
+        this.intervalMergingRule = mergeRule;
         this.locations.addAll(locations);
         this.isRegionUnmapped = checkUnmappedStatus();
 
@@ -75,12 +77,12 @@ public class FilePointer {
         }
     }
 
-    public FilePointer( final GenomeLoc... locations ) {
+    public FilePointer( final IntervalMergingRule mergeRule, final GenomeLoc... locations ) {
-        this(Arrays.asList(locations));
+        this(mergeRule, Arrays.asList(locations));
     }
 
-    public FilePointer( Map<SAMReaderID,SAMFileSpan> fileSpans, List<GenomeLoc> locations ) {
+    public FilePointer( final Map<SAMReaderID,SAMFileSpan> fileSpans, final IntervalMergingRule mergeRule, final List<GenomeLoc> locations ) {
-        this(locations);
+        this(mergeRule, locations);
         this.fileSpans.putAll(fileSpans);
     }
 
@@ -152,6 +154,15 @@ public class FilePointer {
         return locations.size() > 0 ? locations.get(0).getContigIndex() : SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX;
     }
 
+    /**
+     * Returns the IntervalMergingRule used by this FilePointer to merge adjacent locations
+     *
+     * @return the IntervalMergingRule used by this FilePointer (never null)
+     */
+    public IntervalMergingRule getIntervalMergingRule() {
+        return intervalMergingRule;
+    }
+
     /**
      * Is this FilePointer "monolithic"? That is, does it represent all regions in all files that we will
      * ever visit during this GATK run? If this is set to true, the engine will expect to see only this
@@ -277,12 +288,12 @@ public class FilePointer {
      * @return A completely new file pointer that is the combination of the two.
      */
     public FilePointer combine(final GenomeLocParser parser, final FilePointer other) {
-        FilePointer combined = new FilePointer();
+        FilePointer combined = new FilePointer(intervalMergingRule);
 
         List<GenomeLoc> intervals = new ArrayList<GenomeLoc>();
         intervals.addAll(locations);
         intervals.addAll(other.locations);
-        for(GenomeLoc interval: IntervalUtils.sortAndMergeIntervals(parser,intervals,IntervalMergingRule.ALL))
+        for(GenomeLoc interval: IntervalUtils.sortAndMergeIntervals(parser,intervals,intervalMergingRule))
             combined.addLocation(interval);
 
         PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>> thisIterator = new PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>>(this.fileSpans.entrySet().iterator());
@@ -340,15 +351,18 @@ public class FilePointer {
      */
     public static FilePointer union( List<FilePointer> filePointers, GenomeLocParser parser ) {
         if ( filePointers == null || filePointers.isEmpty() ) {
-            return new FilePointer();
+            return new FilePointer(IntervalMergingRule.ALL);
         }
 
         Map<SAMReaderID, List<GATKChunk>> fileChunks = new HashMap<SAMReaderID, List<GATKChunk>>();
         List<GenomeLoc> locations = new ArrayList<GenomeLoc>();
+        IntervalMergingRule mergeRule = filePointers.get(0).getIntervalMergingRule();
 
         // First extract all intervals and file chunks from the FilePointers into unsorted, unmerged collections
         for ( FilePointer filePointer : filePointers ) {
             locations.addAll(filePointer.getLocations());
+            if (mergeRule != filePointer.getIntervalMergingRule())
+                throw new ReviewedStingException("All FilePointers in FilePointer.union() must have use the same IntervalMergeRule");
 
             for ( Map.Entry<SAMReaderID, SAMFileSpan> fileSpanEntry : filePointer.getFileSpans().entrySet() ) {
                 GATKBAMFileSpan fileSpan = (GATKBAMFileSpan)fileSpanEntry.getValue();
@@ -364,7 +378,7 @@ public class FilePointer {
 
         // Now sort and merge the intervals
         List<GenomeLoc> sortedMergedLocations = new ArrayList<GenomeLoc>();
-        sortedMergedLocations.addAll(IntervalUtils.sortAndMergeIntervals(parser, locations, IntervalMergingRule.ALL));
+        sortedMergedLocations.addAll(IntervalUtils.sortAndMergeIntervals(parser, locations, mergeRule));
 
         // For each BAM file, convert from an unsorted, unmerged list of chunks to a GATKBAMFileSpan containing
         // the sorted, merged union of the chunks for that file
@@ -375,7 +389,7 @@ public class FilePointer {
                                 (new GATKBAMFileSpan(unmergedChunks.toArray(new GATKChunk[unmergedChunks.size()]))).union(new GATKBAMFileSpan()));
         }
 
-        return new FilePointer(mergedFileSpans, sortedMergedLocations);
+        return new FilePointer(mergedFileSpans, mergeRule, sortedMergedLocations);
     }
 
     /**

public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.datasources.reads;
 import net.sf.picard.util.PeekableIterator;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 
 import java.util.Iterator;
 
@@ -54,8 +55,8 @@ public class IntervalSharder implements Iterator<FilePointer> {
         return new IntervalSharder(BAMScheduler.createOverMappedReads(dataSource),parser);
     }
 
-    public static IntervalSharder shardOverIntervals(final SAMDataSource dataSource, final GenomeLocSortedSet loci) {
+    public static IntervalSharder shardOverIntervals(final SAMDataSource dataSource, final GenomeLocSortedSet loci, final IntervalMergingRule intervalMergeRule) {
-        return new IntervalSharder(BAMScheduler.createOverIntervals(dataSource,loci),loci.getGenomeLocParser());
+        return new IntervalSharder(BAMScheduler.createOverIntervals(dataSource,intervalMergeRule,loci),loci.getGenomeLocParser());
     }
 
     private IntervalSharder(final BAMScheduler scheduler, final GenomeLocParser parser) {

public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java

@@ -45,6 +45,7 @@ import org.broadinstitute.sting.utils.SimpleTimer;
 import org.broadinstitute.sting.utils.baq.ReadTransformingIterator;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
 import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory;
 
@@ -154,6 +155,11 @@ public class SAMDataSource {
      */
     private final ThreadAllocation threadAllocation;
 
+    /**
+     * How are adjacent intervals merged by the sharder?
+     */
+    private final IntervalMergingRule intervalMergingRule;
+
     /**
      * Static set of unsupported programs that create bam files.
      * The key is the PG record ID and the value is the name of the tool that created it
@@ -217,7 +223,8 @@ public class SAMDataSource {
                 (byte) -1,
                 false,
                 false,
-                null);
+                null,
+                IntervalMergingRule.ALL);
     }
 
     /**
@@ -236,6 +243,7 @@ public class SAMDataSource {
      * @param keepReadsInLIBS should we keep a unique list of reads in LIBS?
      * @param sampleRenameMap Map of BAM file to new sample ID used during on-the-fly runtime sample renaming.
      *                        Will be null if we're not doing sample renaming.
+     * @param intervalMergingRule how are adjacent intervals merged by the sharder
      */
     public SAMDataSource(
             Collection<SAMReaderID> samFiles,
@@ -253,10 +261,12 @@ public class SAMDataSource {
             byte defaultBaseQualities,
             boolean removeProgramRecords,
             final boolean keepReadsInLIBS,
-            final Map<String, String> sampleRenameMap) {
+            final Map<String, String> sampleRenameMap,
+            final IntervalMergingRule intervalMergingRule) {
 
         this.readMetrics = new ReadMetrics();
         this.genomeLocParser = genomeLocParser;
+        this.intervalMergingRule = intervalMergingRule;
 
         readerIDs = samFiles;
 
@@ -1182,7 +1192,7 @@ public class SAMDataSource {
     public Iterable<Shard> createShardIteratorOverIntervals(final GenomeLocSortedSet intervals,final ShardBalancer shardBalancer) {
         if(intervals == null)
             throw new ReviewedStingException("Unable to create schedule from intervals; no intervals were provided.");
-        shardBalancer.initialize(this,IntervalSharder.shardOverIntervals(SAMDataSource.this,intervals),genomeLocParser);
+        shardBalancer.initialize(this,IntervalSharder.shardOverIntervals(SAMDataSource.this,intervals,intervalMergingRule),genomeLocParser);
         return shardBalancer;
     }
 }

public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java

@@ -104,7 +104,7 @@ public class FindLargeShards extends CommandLineProgram {
 
         logger.info(String.format("PROGRESS: Calculating mean and variance: Contig\tRegion.Start\tRegion.Stop\tSize"));        
 
-        IntervalSharder sharder = IntervalSharder.shardOverIntervals(dataSource,intervalSortedSet);
+        IntervalSharder sharder = IntervalSharder.shardOverIntervals(dataSource,intervalSortedSet,IntervalMergingRule.ALL);
         while(sharder.hasNext()) {
             FilePointer filePointer = sharder.next();
 
@@ -133,7 +133,7 @@ public class FindLargeShards extends CommandLineProgram {
         logger.warn(String.format("PROGRESS: Searching for large shards: Contig\tRegion.Start\tRegion.Stop\tSize"));
         out.printf("Contig\tRegion.Start\tRegion.Stop\tSize%n");
 
-        sharder =  IntervalSharder.shardOverIntervals(dataSource,intervalSortedSet);
+        sharder =  IntervalSharder.shardOverIntervals(dataSource,intervalSortedSet,IntervalMergingRule.ALL);
         while(sharder.hasNext()) {
             FilePointer filePointer = sharder.next();
 

public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/ReadMetricsUnitTest.java

@@ -50,6 +50,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
 import org.broadinstitute.sting.utils.activeregion.ActivityProfileState;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.sam.*;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
@@ -158,7 +159,7 @@ public class ReadMetricsUnitTest extends BaseTest {
                 new ValidationExclusion(),
                 new ArrayList<ReadFilter>(),
                 new ArrayList<ReadTransformer>(),
-                false, (byte)30, false, true, null);
+                false, (byte)30, false, true, null, IntervalMergingRule.ALL);
 
         engine.setReadsDataSource(dataSource);
 
@@ -193,7 +194,7 @@ public class ReadMetricsUnitTest extends BaseTest {
                 new ValidationExclusion(),
                 new ArrayList<ReadFilter>(),
                 new ArrayList<ReadTransformer>(),
-                false, (byte)30, false, true, null);
+                false, (byte)30, false, true, null, IntervalMergingRule.ALL);
 
         engine.setReadsDataSource(dataSource);
         final Set<String> samples = SampleUtils.getSAMFileSamples(dataSource.getHeader());
@@ -234,7 +235,7 @@ public class ReadMetricsUnitTest extends BaseTest {
                 new ValidationExclusion(),
                 new ArrayList<ReadFilter>(),
                 new ArrayList<ReadTransformer>(),
-                false, (byte)30, false, true, null);
+                false, (byte)30, false, true, null, IntervalMergingRule.ALL);
 
         engine.setReadsDataSource(dataSource);
         final Set<String> samples = SampleUtils.getSAMFileSamples(dataSource.getHeader());
@@ -281,7 +282,7 @@ public class ReadMetricsUnitTest extends BaseTest {
                 new ValidationExclusion(),
                 filters,
                 new ArrayList<ReadTransformer>(),
-                false, (byte)30, false, true, null);
+                false, (byte)30, false, true, null, IntervalMergingRule.ALL);
 
         engine.setReadsDataSource(dataSource);
 

public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancerUnitTest.java

@@ -31,6 +31,7 @@ import net.sf.samtools.SAMSequenceRecord;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
@@ -82,7 +83,7 @@ public class ActiveRegionShardBalancerUnitTest extends BaseTest {
                 end = myEnd;
                 final GenomeLoc loc = genomeLocParser.createGenomeLoc(record.getSequenceName(), i, myEnd);
                 final Map<SAMReaderID, SAMFileSpan> fileSpans = Collections.emptyMap();
-                final FilePointer fp = new FilePointer(fileSpans, Collections.singletonList(loc));
+                final FilePointer fp = new FilePointer(fileSpans, IntervalMergingRule.ALL, Collections.singletonList(loc));
                 pointers.add(fp);
             }
             expectedLocs.add(Collections.singleton(genomeLocParser.createGenomeLoc(record.getSequenceName(), 0, end)));

public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java

@@ -32,6 +32,7 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -61,12 +62,26 @@ public class FilePointerUnitTest extends BaseTest {
 
     @Test
     public void testFilePointerCombineDisjoint() {
-        FilePointer one = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,5));
+        FilePointer one = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,5));
         one.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,1)));
-        FilePointer two = new FilePointer(genomeLocParser.createGenomeLoc("chr1",6,10));
+        FilePointer two = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",6,10));
         two.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(1,2)));
 
-        FilePointer result = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,10));
+        FilePointer result = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,10));
+        result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,2)));
+
+        Assert.assertEquals(one.combine(genomeLocParser,two),result,"Combination of two file pointers is incorrect");
+        Assert.assertEquals(two.combine(genomeLocParser,one),result,"Combination of two file pointers is incorrect");
+
+        //Now test that adjacent (but disjoint) intervals are properly handled with OVERLAPPING_ONLY
+        one = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY, genomeLocParser.createGenomeLoc("chr1",1,5));
+        one.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,1)));
+        two = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY, genomeLocParser.createGenomeLoc("chr1",6,10));
+        two.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(1,2)));
+
+        result = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY,
+                genomeLocParser.createGenomeLoc("chr1",1,5),
+                genomeLocParser.createGenomeLoc("chr1",6,10));
         result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,2)));
 
         Assert.assertEquals(one.combine(genomeLocParser,two),result,"Combination of two file pointers is incorrect");
@@ -75,12 +90,24 @@ public class FilePointerUnitTest extends BaseTest {
 
     @Test
     public void testFilePointerCombineJoint() {
-        FilePointer one = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,5));
+        FilePointer one = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,5));
         one.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,2)));
-        FilePointer two = new FilePointer(genomeLocParser.createGenomeLoc("chr1",2,6));
+        FilePointer two = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",2,6));
         two.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(1,3)));
 
-        FilePointer result = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,6));
+        FilePointer result = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,6));
+        result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,3)));        
+
+        Assert.assertEquals(one.combine(genomeLocParser,two),result,"Combination of two file pointers is incorrect");
+        Assert.assertEquals(two.combine(genomeLocParser,one),result,"Combination of two file pointers is incorrect");
+
+        //Repeat the tests for OVERLAPPING_ONLY
+        one = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY, genomeLocParser.createGenomeLoc("chr1",1,5));
+        one.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,2)));
+        two = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY, genomeLocParser.createGenomeLoc("chr1",2,6));
+        two.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(1,3)));
+
+        result = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY, genomeLocParser.createGenomeLoc("chr1",1,6));
         result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,3)));
 
         Assert.assertEquals(one.combine(genomeLocParser,two),result,"Combination of two file pointers is incorrect");
@@ -89,12 +116,12 @@ public class FilePointerUnitTest extends BaseTest {
 
     @Test
     public void testFilePointerCombineOneSided() {
-        FilePointer filePointer = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,5));
+        FilePointer filePointer = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,5));
         filePointer.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,1)));
-        FilePointer empty = new FilePointer(genomeLocParser.createGenomeLoc("chr1",6,10));
+        FilePointer empty = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",6,10));
         // Do not add file spans to empty result
 
-        FilePointer result = new FilePointer(genomeLocParser.createGenomeLoc("chr1",1,10));
+        FilePointer result = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,10));
         result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,1)));
         Assert.assertEquals(filePointer.combine(genomeLocParser,empty),result,"Combination of two file pointers is incorrect");
         Assert.assertEquals(empty.combine(genomeLocParser,filePointer),result,"Combination of two file pointers is incorrect");

public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java

@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -184,7 +185,7 @@ public class SAMDataSourceUnitTest extends BaseTest {
                 (byte) -1,
                 removeProgramRecords,
                 false,
-                null);
+                null, IntervalMergingRule.ALL);
 
         List<SAMProgramRecord> dontRemoveProgramRecords = data.getHeader().getProgramRecords();
         assertEquals(dontRemoveProgramRecords, defaultProgramRecords, "testRemoveProgramRecords: default program records differ from removeProgramRecords = false");
@@ -205,7 +206,7 @@ public class SAMDataSourceUnitTest extends BaseTest {
                 (byte) -1,
                 removeProgramRecords,
                 false,
-                null);
+                null, IntervalMergingRule.ALL);
 
         List<SAMProgramRecord> doRemoveProgramRecords = data.getHeader().getProgramRecords();
         assertTrue(doRemoveProgramRecords.isEmpty(), "testRemoveProgramRecords: program records not cleared when removeProgramRecords = true");
@@ -247,6 +248,6 @@ public class SAMDataSourceUnitTest extends BaseTest {
                 (byte) -1,
                 true,
                 false,
-                null);
+                null, IntervalMergingRule.ALL);
     }
 }

public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java

@@ -481,7 +481,7 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
                 new ValidationExclusion(),
                 new ArrayList<ReadFilter>(),
                 new ArrayList<ReadTransformer>(),
-                false, (byte)30, false, true, null);
+                false, (byte)30, false, true, null, IntervalMergingRule.ALL);
 
         engine.setReadsDataSource(dataSource);
         final Set<String> samples = SampleUtils.getSAMFileSamples(dataSource.getHeader());

public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java

@@ -120,6 +120,28 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
         execute("testNoCoverageDueToFiltering",spec);
     }
 
+    @Test
+    public void testAdjacentIntervals() {
+        String[] intervals = {"chr1:1-999", "chr1:1000-65536", "chr1:65537-80000", "chr1:80001-81000"};
+        String[] bams = {publicTestDir+"exampleBAM.bam"};
+
+        String cmd = buildRootCmd(exampleFASTA, new ArrayList<String>(Arrays.asList(bams)), new ArrayList<String>(Arrays.asList(intervals))) + " -im OVERLAPPING_ONLY";
+        WalkerTestSpec spec = new WalkerTestSpec(cmd, 0, new ArrayList<String>());
+
+        File baseOutputFile = WalkerTest.createTempFile("depthofcoverageadjinterval", ".tmp");
+        spec.setOutputFileLocation(baseOutputFile);
+
+        spec.addAuxFile("84b95d62f53e28919d1b5286558a1cae", baseOutputFile);
+        spec.addAuxFile("e445d4529dd3e3caa486ab8f5ec63e49", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
+        spec.addAuxFile("b69c89ba8b0c393b735616c2bc3aea76", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
+        spec.addAuxFile("788988dac6119a02de2c8d4dfb06b727", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
+        spec.addAuxFile("3769ed40ab3ccd2ed94a9dc05cc2bc2f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
+        spec.addAuxFile("1281605e022d7462fbbcd14de53d1ca3", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
+        spec.addAuxFile("4b41d6ff88aa2662697cb7e4b5346cb8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
+
+        execute("testAdjacentIntervals", spec);
+    }
+
     public void testRefNHandling(boolean includeNs, final String md5) {
         String command = "-R " + b37KGReference + " -L 20:26,319,565-26,319,575 -I " + validationDataLocation + "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -T DepthOfCoverage -baseCounts --omitIntervalStatistics --omitLocusTable --omitPerSampleStats -o %s";
         if ( includeNs ) command += " --includeRefNSites";