Index: src/core/org/terrier/structures/indexing/singlepass/hadoop/Hadoop_BasicSinglePassIndexer.java
===================================================================
--- src/core/org/terrier/structures/indexing/singlepass/hadoop/Hadoop_BasicSinglePassIndexer.java	(revision 3953)
+++ src/core/org/terrier/structures/indexing/singlepass/hadoop/Hadoop_BasicSinglePassIndexer.java	(working copy)
@@ -105,6 +105,12 @@
 	implements Mapper<Text, SplitAwareWrapper<Document>, SplitEmittedTerm, MapEmittedPostingList>,
 	Reducer<SplitEmittedTerm, MapEmittedPostingList, Object, Object>
 {
+
+	/** TREC-388: disable per-flush compression of docids, as docid alignment problems
+	  * can arise if map tasks are restarted. Be vary careful of changing this.
+	  */
+	static final boolean RESET_IDS_ON_FLUSH = false;
+	
 	/**
 	 * main
 	 * @param args
@@ -304,6 +310,7 @@
 			value="DM_GC",
 			justification="Forcing GC is an essential part of releasing" +
 					"memory for further indexing")
+	@Override
 	/** causes the posting lists built up in memory to be flushed out */
 	protected void forceFlush() throws IOException
 	{
@@ -318,9 +325,10 @@
 		createMemoryPostings();
 		memoryCheck.reset();
 		numberOfDocsSinceFlush = 0;
-		currentId = 0;
+		if (RESET_IDS_ON_FLUSH)
+			currentId = 0;
 		flushNo++;
-	}	
+	}
 	
 	/**
 	 * Map processes a single document. Stores the terms in the document along with the posting list
@@ -526,7 +534,7 @@
 			logger.info("Run data file "+ file.getPath().toString()+" has length "+Files.length(file.getPath().toString()));
 			runDataIn = new DataInputStream(Files.openFileStream(file.getPath().toString()));
 			tempHRD = new MapData(runDataIn);
-			//check to see if this file contaned our split information
+			//check to see if this file contained our split information
 			if (mutipleIndices && partitionChecker.calculatePartition(tempHRD.getSplitnum(), jc.getNumReduceTasks()) != thisPartition)
 				continue;
 			
@@ -605,7 +613,6 @@
 		logger.info("Merging document and meta indices");
 		final DocumentIndexBuilder docidOutput = new DocumentIndexBuilder(currentIndex, "document");
 		final MetaIndexBuilder metaBuilder = this.createMetaIndexBuilder();
-		//int i_index = 0;
 		int docCount =-1;
 		TerrierTimer tt = new TerrierTimer("Merging document & meta indices", numdocs);
 		tt.start();
@@ -624,7 +631,6 @@
 				}
 			    IndexUtil.close(docidInput);
 			    IndexUtil.close(metaInput1);
-			    //i_index++;
 			}
 		} finally {
 			tt.finished();
@@ -639,6 +645,13 @@
 		{
 			currentIndex.addIndexStructure("document-factory", SimpleDocumentIndexEntry.Factory.class.getName(), "", "");
 		}
+		
+		//check document counts
+		if (docCount != numdocs)
+		{
+			logger.warn("Mismatch between expected ("+numdocs+") and found document counts ("+docCount+")");
+		}
+		
 		logger.info("Finished merging document indices from "+src.length+" map tasks: "+docCount +" documents found");
 	}
 
@@ -687,6 +700,12 @@
 		currentIndex.setIndexProperty("num.Pointers",""+lexstream.getNumberOfPointersWritten() );
 		if (FieldScore.FIELDS_COUNT > 0)
 			currentIndex.addIndexStructure("lexicon-valuefactory", FieldLexiconEntry.Factory.class.getName(), "java.lang.String", "${index.inverted.fields.count}");
+		
+		if (lexstream.getNumberOfTermsWritten() == 0)
+		{
+			logger.warn("Lexicon wrote no terms, but reduceStarted = "+ reduceStarted);
+		}
+		
 		this.finishedInvertedIndexBuild();
 			
 		
Index: src/core/org/terrier/structures/indexing/singlepass/hadoop/HadoopRunsMerger.java
===================================================================
--- src/core/org/terrier/structures/indexing/singlepass/hadoop/HadoopRunsMerger.java	(revision 3953)
+++ src/core/org/terrier/structures/indexing/singlepass/hadoop/HadoopRunsMerger.java	(working copy)
@@ -153,18 +153,22 @@
 		if (correctHRD == null)
 			throw new IOException("Did not find map data for split "+ splitNo);
 		
-		// Add the FlushShift
 		int currentFlushDocs=0;
-		ListIterator<Integer> LI = correctHRD.getFlushDocSizes().listIterator(0);
-		//System.out.println("Runs Flush number : "+run.getRunNo()+", Size of HRD :"+correctHRD.getFlushDocSizes().size());
-		int currentFlush =0;
-		while (currentFlush<flushNumber) {
-			//System.out.println("Runs Flush number : "+run.getRunNo()+", FlushCheck : "+currentFlush+", Size of HRD :"+correctHRD.getFlushDocSizes().size());
-			currentFlushDocs += LI.next(); 
-			currentFlush++;
+		// Add the FlushShift, if configured to do so 
+		if (Hadoop_BasicSinglePassIndexer.RESET_IDS_ON_FLUSH)
+		{		
+			
+			ListIterator<Integer> LI = correctHRD.getFlushDocSizes().listIterator(0);
+			//System.out.println("Runs Flush number : "+run.getRunNo()+", Size of HRD :"+correctHRD.getFlushDocSizes().size());
+			int currentFlush =0;
+			while (currentFlush<flushNumber) {
+				//System.out.println("Runs Flush number : "+run.getRunNo()+", FlushCheck : "+currentFlush+", Size of HRD :"+correctHRD.getFlushDocSizes().size());
+				currentFlushDocs += LI.next(); 
+				currentFlush++;
+			}		
 		}
+		return NumPreDocs+currentFlushDocs;
 		
-		return NumPreDocs+currentFlushDocs;
 	}
 
 }