diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriter.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriter.java
new file mode 100644
index 000000000..f83560a4a
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriter.java
@@ -0,0 +1,76 @@
+package org.broadinstitute.sting.utils.sam;
+
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMRecord;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/*
+ * Copyright (c) 2009 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.
+ */
+
+/**
+ * @author aaron
+ *
+ * Class ArtificialSAMFileWriter
+ *
+ * generates a fike samwriter, that you can get the output reads
+ * from when you're done.
+ */
+public class ArtificialSAMFileWriter implements SAMFileWriter {
+
+ // are we closed
+ private boolean closed = false;
+
+ // the SAMRecords we've added to this writer
+ List records = new ArrayList();
+
+ public void addAlignment( SAMRecord alignment ) {
+ records.add(alignment);
+ }
+
+ /** not much to do when we're fake */
+ public void close() {
+ closed = true;
+ }
+
+ /**
+ * are we closed?
+ *
+ * @return true if we're closed
+ */
+ public boolean isClosed() {
+ return closed;
+ }
+
+ /**
+ * get the records we've seen
+ * @return
+ */
+ public List getRecords() {
+ return records;
+ }
+}
diff --git a/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterTest.java b/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterTest.java
new file mode 100644
index 000000000..ff7a44a0a
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterTest.java
@@ -0,0 +1,95 @@
+package org.broadinstitute.sting.utils.sam;
+
+import org.junit.Before;
+import org.junit.Test;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import org.broadinstitute.sting.BaseTest;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMFileHeader;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+/*
+ * Copyright (c) 2009 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.
+ */
+
+/**
+ * @author aaron
+ *
+ * Class ArtificialSAMFileWriter
+ *
+ * Test out the ArtificialSAMFileWriter class
+ */
+public class ArtificialSAMFileWriterTest extends BaseTest {
+
+ /** the artificial sam writer */
+ private ArtificialSAMFileWriter writer;
+ private SAMFileHeader header;
+ private final int startChr = 1;
+ private final int numChr = 2;
+ private final int chrSize = 100;
+
+ @Before
+ public void before() {
+ writer = new ArtificialSAMFileWriter();
+ header = ArtificialSamUtils.createArtificialSamHeader(numChr, startChr, chrSize);
+ }
+
+ @Test
+ public void testBasicCount() {
+ for (int x = 0; x < 100; x++) {
+ SAMRecord rec = ArtificialSamUtils.createArtificialRead(header, String.valueOf(x), 1, x, ArtificialSamUtils.DEFAULT_READ_LENGTH);
+ writer.addAlignment(rec);
+ }
+ assertEquals(100, writer.getRecords().size());
+
+ }
+
+ @Test
+ public void testReadName() {
+ List names = new ArrayList();
+
+ for (int x = 0; x < 100; x++) {
+ names.add(String.valueOf(x));
+ SAMRecord rec = ArtificialSamUtils.createArtificialRead(header, String.valueOf(x), 1, x, ArtificialSamUtils.DEFAULT_READ_LENGTH);
+ writer.addAlignment(rec);
+ }
+ assertEquals(100, writer.getRecords().size());
+
+ // check the names
+ for (int x = 0; x < 100; x++) {
+ assertTrue(names.get(x).equals(writer.getRecords().get(x).getReadName()));
+ }
+
+ }
+
+ @Test
+ public void testClose() {
+ writer.close();
+ assertTrue(writer.isClosed());
+ }
+}