reference sequence file for CRAM format

uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java

+/* BamView
+ *
+ * created: 2012
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2012  Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.components.alignment;
+
+import net.sf.picard.reference.ReferenceSequence;
+import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.samtools.SAMSequenceDictionary;
+import uk.ac.sanger.artemis.Entry;
+import uk.ac.sanger.artemis.io.Range;
+import uk.ac.sanger.artemis.sequence.Bases;
+import uk.ac.sanger.artemis.util.OutOfRangeException;
+
+
+  class CRAMReferenceSequenceFile implements ReferenceSequenceFile
+  {
+    private Entry sequence;
+    private BamView bamView;
+    
+    CRAMReferenceSequenceFile(final Entry sequence, final BamView bamView)
+    {
+      this.sequence = sequence;
+      this.bamView  = bamView;
+    }
+    
+    /**
+    * Retrieves the complete sequence described by this contig.
+    * @param contig contig whose data should be returned.
+    * @return The full sequence associated with this contig.
+    * @throws UnsupportedOperationException if !sIndexed.
+    */
+    public ReferenceSequence getSequence(String contig)
+    {
+      return getSubsequenceAt(contig, 1L, sequence.getBases().getLength());
+      
+      //return new ReferenceSequence(sequence.getName(), 0, 
+      //    sequence.getBases().getForwardStrand().getStrandBases().getBytes());
+    }
+
+    public SAMSequenceDictionary getSequenceDictionary()
+    {
+      return null;
+    }
+
+    /**
+    * Gets the subsequence of the contig in the range [start,stop]
+    * @param contig Contig whose subsequence to retrieve.
+    * @param start inclusive, 1-based start of region.
+    * @param stop inclusive, 1-based stop of region.
+    * @return The partial reference sequence associated with this range.
+    * @throws UnsupportedOperationException if !sIndexed.
+    */
+    public ReferenceSequence getSubsequenceAt(String contig, long start, long stop )
+    {
+      try
+      {
+        if(bamView.isConcatSequences())
+        {
+          int offset = bamView.getSequenceOffset(contig);
+          start += offset;
+          stop  += offset;
+        }
+        
+        return new ReferenceSequence(sequence.getName(), 0, 
+            sequence.getBases().getSubSequence(new Range((int)start, (int)stop), Bases.FORWARD).getBytes());
+      }
+      catch (OutOfRangeException e)
+      {
+        e.printStackTrace();
+      }
+      return null;
+    }
+
+    /**
+    * @return true if getSequence and getSubsequenceAt methods are allowed.
+    */
+    public boolean isIndexed()
+    {
+      return true;
+    }
+
+    public ReferenceSequence nextSequence()
+    {
+      return null;
+    }
+
+    public void reset()
+    {
+    }
+    
+  }
\ No newline at end of file