diff --git a/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java b/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
new file mode 100644
index 000000000..64b20a308
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+++ b/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
@@ -0,0 +1,147 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.sam;
+
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMFileWriterFactory;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
+import java.io.File;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: asivache
+ * Date: May 31, 2011
+ * Time: 3:52:49 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class NWaySAMFileWriter implements SAMFileWriter {
+
+    private Map<SAMReaderID,SAMFileWriter> writerMap = null;
+    private boolean presorted ;
+    GenomeAnalysisEngine toolkit;
+
+    public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted) {
+        this.presorted = presorted;
+        this.toolkit = toolkit;
+        writerMap = new HashMap<SAMReaderID,SAMFileWriter>();
+        setupByReader(toolkit,in2out,order, presorted);
+    }
+
+    public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted) {
+        this.presorted = presorted;
+        this.toolkit = toolkit;
+        writerMap = new HashMap<SAMReaderID,SAMFileWriter>();
+        setupByReader(toolkit,ext,order, presorted);
+    }
+
+    /**
+     * Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK engine (those will be retrieved
+     * from <code>toolkit</code>). The <code>in2out</code> map must contain an entry for each input filename and map it
+     * onto a unique output file name.
+     * @param toolkit
+     * @param in2out
+     */
+    public void setupByReader(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted) {
+
+        if ( in2out==null ) throw new StingException("input-output bam filename map for n-way-out writing is NULL");
+        for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) {
+
+            String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();
+
+            String outName;
+            if ( ! in2out.containsKey(fName) )
+                    throw new UserException.BadInput("Input-output bam filename map does not contain an entry for the input file "+fName);
+            outName = in2out.get(fName);
+
+            if ( writerMap.containsKey( rid ) )
+                throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
+
+            addWriter(rid,outName, order, presorted);
+        }
+
+    }
+
+    /**
+     * Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK engine (those will be retrieved
+     * from <code>toolkit</code>). The output file names will be generated automatically by stripping ".sam" or ".bam" off the
+     * input file name and adding ext instead (e.g. ".cleaned.bam").
+     * onto a unique output file name.
+     * @param toolkit
+     * @param ext
+     */
+    public void setupByReader(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted) {
+        for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) {
+
+            String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();
+
+            String outName;
+            int pos ;
+            if ( fName.toUpperCase().endsWith(".BAM") ) pos = fName.toUpperCase().lastIndexOf(".BAM");
+            else {
+                if ( fName.toUpperCase().endsWith(".SAM") ) pos = fName.toUpperCase().lastIndexOf(".SAM");
+                else throw new UserException.BadInput("Input file name "+fName+" does not end with .sam or .bam");
+            }
+            String prefix = fName.substring(0,pos);
+            outName = prefix+ext;
+
+            if ( writerMap.containsKey( rid ) )
+                throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
+
+            addWriter(rid,outName, order, presorted);
+        }
+
+    }
+
+    private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted) {
+        File f = new File(outName);
+        SAMFileHeader header = toolkit.getSAMFileHeader(id).clone();
+        header.setSortOrder(order);
+        SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, presorted, f);
+        writerMap.put(id,sw);
+    }
+
+    
+    public void addAlignment(SAMRecord samRecord) {
+        final SAMReaderID id = toolkit.getReaderIDForRead(samRecord);
+        writerMap.get(id).addAlignment(samRecord);
+    }
+
+    public SAMFileHeader getFileHeader() {
+        return toolkit.getSAMFileHeader();  
+    }
+
+    public void close() {
+        for ( SAMFileWriter w : writerMap.values() ) w.close();
+    }
+}