diff --git a/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java b/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java
index 83e69c035..5d7c799c3 100755
--- a/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java
@@ -24,14 +24,15 @@ public class IndelInspectorMain extends CommandLineProgram {
     @Option(shortName="I", doc="SAM or BAM file for calling",optional=true) public File INPUT_FILE;
     @Option(shortName="L",doc="Genomic interval to run on, as contig[:start[-stop]]; whole genome if not specified", optional=true) public String GENOME_LOCATION;
     @Option(shortName="V",doc="Verbosity level: SILENT, PILESUMMARY, ALIGNMENTS", optional=true) public String VERBOSITY_LEVEL;
-    @Option(doc="Output file (sam or bam) for non-indel related reads and indel reads that were not improved") public String OUT1; 
+    @Option(doc="Output file (sam or bam) for non-indel related reads and indel reads that were not improved (see OUTF)") public String OUT1; 
     @Option(doc="Output file (sam or bam) for improved (realigned) indel related reads") public String OUT2;
+    @Option(doc="Output file (sam or bam) for indel related reads that fail to realign", optional = true ) public String OUTF;
     @Option(doc="[paranoid] If true, all reads that would be otherwise picked and processed by this tool will be saved, unmodified, into OUT1", optional=true) public Boolean CONTROL_RUN;
     @Option(doc="Error counting mode: MM - mismatches only (from sam tags), MC - mismatches only doing actual mismatch count on the fly (use this if tags are incorrectly set); ERR - errors (arachne style: mm+gap lengths), MG - count mismatches and gaps as one error each") public String ERR_MODE;
     @Option(doc="Maximum number of errors allowed (see ERR_MODE)") public Integer MAX_ERRS;
     @Option(shortName="R", doc="Reference fasta or fasta.gz file") public File REF_FILE;
     @Option(doc="Ignore reads that are longer than the specified cutoff (not a good way to do things but might be necessary because of performance issues)", optional=true) public Integer MAX_READ_LENGTH;
-    @Option(doc="Realignment will be attempted around trains of indels with at least of them observed COUNT_CUTOFF times or more",optional=true) public Integer COUNT_CUTOFF;
+    @Option(doc="Realignment will be attempted around trains of indels with at least one indel observed COUNT_CUTOFF times or more",optional=true) public Integer COUNT_CUTOFF;
 
     /** Required main method implementation. */
     public static void main(final String[] argv) {
@@ -60,6 +61,8 @@ public class IndelInspectorMain extends CommandLineProgram {
             location = GenomeLoc.parseGenomeLoc(GENOME_LOCATION);
         }
         
+        if ( COUNT_CUTOFF == null ) COUNT_CUTOFF = 2;
+        
         if ( ! ERR_MODE.equals("MM") && ! ERR_MODE.equals("MG") && ! ERR_MODE.equals("ERR") && ! ERR_MODE.equals("MC") ) {
             System.out.println("Unknown value specified for ERR_MODE: "+ERR_MODE);
             return 1;
@@ -77,9 +80,11 @@ public class IndelInspectorMain extends CommandLineProgram {
 
         IndelRecordPileCollector col = null;
         PassThroughWriter ptWriter = new PassThroughWriter(OUT1,samReader.getFileHeader());
+        PassThroughWriter ptFailedWriter = null;
+        if ( OUTF != null ) ptFailedWriter = new PassThroughWriter(OUTF,samReader.getFileHeader());
         PileBuilder pileBuilder = null;
         if ( CONTROL_RUN == null ) CONTROL_RUN=false;
-        if ( ! CONTROL_RUN ) pileBuilder = new PileBuilder(OUT2,samReader.getFileHeader(),ptWriter);
+        if ( ! CONTROL_RUN ) pileBuilder = new PileBuilder(OUT2,samReader.getFileHeader(), ptFailedWriter == null? ptWriter : ptFailedWriter);
 
         try {
             if ( CONTROL_RUN ) col = new IndelRecordPileCollector(ptWriter, new DiscardingPileReceiver() );
diff --git a/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java b/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
index 0d55bdbe4..c8c3d479b 100755
--- a/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
@@ -357,11 +357,16 @@ public class PileBuilder implements RecordPileReceiver {
                 int id = id_iter.next();
 
                 SAMRecord r = as_list.get(id);
-                if ( pile_failed || pile_unmodified ) {
+                if ( pile_failed  ) {
                     failedPileReceiver.receive(r); // nothing to do, send failed piles directly for writing
                     continue;
                 }
 
+                if (  pile_unmodified ) {
+                    samWriter.addAlignment(r); // nothing to do, "cleaned" pile has not changed, so we just write all reads back
+                    continue;
+                }
+
                 // we improved stuff!! let's reset the alignment parameters!
                 int cons_offset = ma.getOffsetWrtConsensus(id); // offset of the read 'id' wrt multiple alignment's full consensus seq