First working code to use SamRecordFactory to produce objects of our own design in SAMFileReader

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java

@@ -43,6 +43,7 @@ import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.baq.BAQSamIterator;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory;
 
 import java.io.File;
 import java.lang.reflect.InvocationTargetException;
@@ -57,6 +58,8 @@ import java.util.*;
  * Converts shards to SAM iterators over the specified region
  */
 public class SAMDataSource {
+    final private static GATKSamRecordFactory factory = new GATKSamRecordFactory();
+
     /** Backing support for reads. */
     protected final ReadProperties readProperties;
 
@@ -756,6 +759,7 @@ public class SAMDataSource {
         public SAMReaders(Collection<SAMReaderID> readerIDs, SAMFileReader.ValidationStringency validationStringency) {
             for(SAMReaderID readerID: readerIDs) {
                 SAMFileReader reader = new SAMFileReader(readerID.samFile);
+                reader.setSAMRecordFactory(factory);
                 reader.enableFileSource(true);
                 reader.enableIndexMemoryMapping(false);
                 if(!enableLowMemorySharding)

public/java/src/org/broadinstitute/sting/utils/sam/GATKSamRecordFactory.java

@@ -0,0 +1,74 @@
+/*
+ * Copyright (c) 2011, 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.SAMRecord;
+import net.sf.samtools.SAMRecordFactory;
+import net.sf.samtools.BAMRecord;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
+/**
+ * Factory interface which allows plugging in of different classes for generating instances of
+ * SAMRecord and BAMRecord when reading from SAM/BAM files.
+ *
+ * @author Tim Fennell
+ */
+public class GATKSamRecordFactory implements SAMRecordFactory {
+
+    /** Create a new SAMRecord to be filled in */
+    public SAMRecord createSAMRecord(SAMFileHeader header) {
+        throw new UserException.BadInput("The GATK now longer supports input SAM files");
+    }
+
+    /** Create a new BAM Record. */
+    public BAMRecord createBAMRecord(final SAMFileHeader header,
+                                     final int referenceSequenceIndex,
+                                     final int alignmentStart,
+                                     final short readNameLength,
+                                     final short mappingQuality,
+                                     final int indexingBin,
+                                     final int cigarLen,
+                                     final int flags,
+                                     final int readLen,
+                                     final int mateReferenceSequenceIndex,
+                                     final int mateAlignmentStart,
+                                     final int insertSize,
+                                     final byte[] variableLengthBlock) {
+        return new BAMRecord(header,
+                             referenceSequenceIndex,
+                             alignmentStart,
+                             readNameLength,
+                             mappingQuality,
+                             indexingBin,
+                             cigarLen,
+                             flags,
+                             readLen,
+                             mateReferenceSequenceIndex,
+                             mateAlignmentStart,
+                             insertSize,
+                             variableLengthBlock);
+    }
+}