Skip to content
Snippets Groups Projects
Commit 2c326dc9 authored by tcarver's avatar tcarver
Browse files

reference sequence file for CRAM format

parent 23f98074
No related branches found
No related tags found
No related merge requests found
/* 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
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment