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/* 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
{
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{
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()
{
}
}