diff --git a/java/src/org/broadinstitute/sting/playground/indels/ShowMSA.java b/java/src/org/broadinstitute/sting/playground/indels/ShowMSA.java
new file mode 100755
index 000000000..cdc0033e1
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/indels/ShowMSA.java
@@ -0,0 +1,229 @@
+package org.broadinstitute.sting.playground.indels;
+
+import java.io.File;
+
+import edu.mit.broad.picard.reference.*;
+import edu.mit.broad.picard.cmdline.CommandLineProgram;
+import edu.mit.broad.picard.cmdline.Option;
+import edu.mit.broad.picard.cmdline.Usage;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+
+public class ShowMSA extends CommandLineProgram {
+
+    // Usage and parameters
+    @Usage(programVersion="1.0") public String USAGE = "Prints MSA into stdout\n";
+    @Option(shortName="I", doc="SAM or BAM file with alignment data") public File INPUT_FILE;
+    @Option(shortName="L", doc="Contig:Start-Stop or Contig:poslocation of the window to draw") public String LOCATION;
+    @Option(shortName="W", doc="Number of bases on each side of specified position if LOCATION is in Contig:pos format; ignored otherwise", optional=true) public Integer WINDOW;
+    @Option(shortName="R", doc="Reference fastb file") public File REF_FILE;
+    @Option(shortName="P", doc="If true, then any read (partially) overlapping with the specified region will be shown. "+
+    		"Otherwise (default), only reads fully contained in the specified interval are shown", optional=true) public Boolean PARTIAL;
+    @Option(doc="Error counting mode: MM - count mismatches only, ERR - count errors (arachne style), 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="F",doc="Format: PILE - show alignment, FASTA - print sequences in fasta",optional=true) public String OUT_FORMAT;
+
+    /** Required main method implementation. */
+    public static void main(final String[] argv) {
+        System.exit(new ShowMSA().instanceMain(argv));
+    }
+    
+	protected int doWork() {
+		
+		if ( ! ERR_MODE.equals("MM") && ! ERR_MODE.equals("MG") && ! ERR_MODE.equals("ERR") ) {
+			System.out.println("Unknown value specified for ERR_MODE");
+			return 1;
+		}
+
+		if ( PARTIAL == null ) PARTIAL = new Boolean(false);
+		if ( OUT_FORMAT == null ) OUT_FORMAT=new String("PILE");
+		
+		if ( ! OUT_FORMAT.equals("PILE") && ! OUT_FORMAT.equals("FASTA")) {
+			System.out.println("OUT_FORMAT can only have values PILE or FASTA");
+			return 1;
+		}
+		
+		if ( ! INPUT_FILE.exists() ) {
+			System.out.println("Specified INPUT_FILE does not exist");
+			return 1;
+		}
+
+		if ( ! REF_FILE.exists() ) {
+			System.out.println("Specified REF_FILE does not exist");
+			return 1;
+		}
+
+		if ( LOCATION.indexOf(':') == -1 ) {
+			System.out.println("LOCATION should follow Contig:Start-Stop or Contig:Pos format");
+			return 1;
+		}
+		String[] s1 = LOCATION.split(":");
+		int contig;
+		try {
+			contig = Integer.valueOf(s1[0]);
+		}	catch (NumberFormatException e) {
+			System.out.println("LOCATION: contig must be specified as an integer");
+			return 1;
+		}
+		
+		if ( s1.length != 2 ) {
+			System.out.println("LOCATION should follow Contig:Start-Stop or Contig:Pos format");
+			return 1;
+		}
+		
+		String s2[] = s1[1].split("-");
+		if ( s2.length > 2 ) {
+			System.out.println("LOCATION should follow Contig:Start-Stop or Contig:Pos format");
+			return 1;
+		}
+		int left, right;
+		if ( s2.length == 2 ) {
+			try {
+				left = Integer.valueOf(s2[0]);
+				right = Integer.valueOf(s2[1]);
+			}	catch (NumberFormatException e) {
+				System.out.println("LOCATION: window boundaries should be specified as integers");
+				return 1;
+			}
+		} else {
+			int pos = 0;
+			try {
+				pos = Integer.valueOf(s2[0]);
+			}	catch (NumberFormatException e) {
+				System.out.println("LOCATION: position on the contig should be specified as an integer");
+				return 1;
+			}
+			if (WINDOW == null ) {
+				System.out.println("WINDOW must be specified when LOCATION specifies a single poisiton (Contig:Pos)");
+				return 1;
+			}
+			left = pos - WINDOW.intValue();
+			right = pos+WINDOW.intValue();
+		}
+		
+		
+		String ref_contig ;
+		
+		try {
+		    ReferenceSequenceFileWalker mRefReader =
+                    new ReferenceSequenceFileWalker(ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE));
+			ref_contig = mRefReader.get(contig).toString(); // reload ref
+		} catch (Exception e) {
+			System.out.println("Failed to read reference sequence from " + REF_FILE);
+			return 1;
+		}
+
+		SAMFileReader reader ;
+		try {
+			reader = new SAMFileReader(INPUT_FILE);
+		} catch ( Exception e) {
+			System.out.println(e.getMessage());
+			return 1;
+		}
+		
+		SequencePile msa=null;
+		
+		if ( OUT_FORMAT.equals("PILE")) {
+			msa = new SequencePile(ref_contig.substring(left-1, right));
+		} else {
+			System.out.println(">reference "+contig+":"+left+"-"+right);
+			System.out.println(ref_contig.substring(left-1, right));
+		}
+		
+		for( SAMRecord r : reader ) {
+			if ( r.getReadUnmappedFlag() ) continue;
+			if ( r.getReferenceIndex() < contig ) continue;
+			if ( r.getReferenceIndex() > contig ) break;
+			if ( r.getAlignmentEnd() < left ) continue;
+			if ( r.getAlignmentStart() >= right ) break;
+			if ( ! PARTIAL && ( r.getAlignmentStart() < left || r.getAlignmentEnd() >= right ) ) continue;
+			
+        	int err = -1;
+        	if ( ERR_MODE.equals("MM")) err = numMismatches(r);
+        	else if ( ERR_MODE.equals("ERR")) err = numErrors(r);
+        	else if ( ERR_MODE.equals("MG")) err = numMismatchesGaps(r);
+        	if ( err > MAX_ERRS ) continue;
+
+        	if ( OUT_FORMAT.equals("PILE") ) {
+        		msa.addAlignedSequence(r.getReadString(), r.getReadNegativeStrandFlag(), r.getCigar(), r.getAlignmentStart() - left);
+        	} else {
+        		System.out.print(">read "+r.getReadName());
+        		if ( r.getReadNegativeStrandFlag() ) System.out.println("(rc)");
+        		else System.out.println("(fw)");
+        		System.out.println(r.getReadString());
+        	}
+		}
+		
+		if ( OUT_FORMAT.equals("PILE") ) msa.colorprint();
+////			System.out.println(msa.format());
+		
+		return 0;
+	}
+
+	/** This method is a HACK: it is designed to work around the current bug in NM tags created  at CRD 
+	 * 
+	 * @param r SAM record that must specify an alignment
+	 * @return number of errors (number of mismatches plus total length of all insertions/deletions
+	 * @throws RuntimeException if cigar contains any elements other than M,I,D
+	 */
+	private static int numErrors(SAMRecord r) throws RuntimeException {
+		
+		// NM currently stores the total number of mismatches in all blocks + 1
+		int errs = numMismatches(r);
+		
+		// now we have to add the total length of all indels:
+		Cigar c = r.getCigar();
+		for ( int i = 0 ; i < c.numCigarElements() ; i++ ) {
+			CigarElement ce = c.getCigarElement(i);
+			switch( ce.getOperator()) {
+			case M : break; // we already have correct number of mismatches
+			case I : 
+			case D :
+					errs += ce.getLength();
+					break;
+			default: throw new RuntimeException("Unrecognized cigar element");
+			}
+		}
+		return errs;
+	}
+
+	/** This method is a HACK: it is designed to work around the current bug in NM tags created  at CRD 
+	 * 
+	 * @param r SAM record that must specify an alignment
+	 * @return number of errors (number of mismatches plus total number of all insertions/deletions (each insertion or
+	 * deletion will be counted as a single error regardless of the length)
+	 * @throws RuntimeException if cigar contains any elements other than M,I,D
+	 */
+	private static int numMismatchesGaps(SAMRecord r) throws RuntimeException {
+		
+		// NM currently stores the total number of mismatches in all blocks + 1
+		int errs = numMismatches(r);
+		
+		// now we have to add the total length of all indels:
+		Cigar c = r.getCigar();
+		for ( int i = 0 ; i < c.numCigarElements() ; i++ ) {
+			CigarElement ce = c.getCigarElement(i);
+			switch( ce.getOperator()) {
+			case M : break; // we already have correct number of mismatches
+			case I : 
+			case D :
+					errs++;
+					break;
+			default: throw new RuntimeException("Unrecognized cigar element");
+			}
+		}
+		return errs;
+	}
+	
+	
+	/** This method is a HACK: it is designed to work around the current bug in NM tags created  at CRD */
+	private static int numMismatches(SAMRecord r) throws RuntimeException {
+		
+		// NM currently stores the total number of mismatches in all blocks + 1
+		return ((Integer)r.getAttribute("NM")).intValue() - 1;
+		
+	}
+	
+}