adding an artificial sam file writer, used to unit test some of the walkers (mainly the PrintReadsWalker)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@956 348d0f76-0448-11de-a6fe-93d51630548a

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
+ *         <p/>
+ *         Class ArtificialSAMFileWriter
+ *         <p/>
+ * 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<SAMRecord> records = new ArrayList<SAMRecord>();
+
+    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<SAMRecord> getRecords() {
+        return records;
+    }
+}

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
+ *         <p/>
+ *         Class ArtificialSAMFileWriter
+ *         <p/>
+ *         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<String> names = new ArrayList<String>();
+
+        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());
+    }
+}