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1   /*--------------------------------------------------------------------------
2    *  Copyright 2010 utgenome.org
3    *
4    *  Licensed under the Apache License, Version 2.0 (the "License");
5    *  you may not use this file except in compliance with the License.
6    *  You may obtain a copy of the License at
7    *
8    *     http://www.apache.org/licenses/LICENSE-2.0
9    *
10   *  Unless required by applicable law or agreed to in writing, software
11   *  distributed under the License is distributed on an "AS IS" BASIS,
12   *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13   *  See the License for the specific language governing permissions and
14   *  limitations under the License.
15   *--------------------------------------------------------------------------*/
16  //--------------------------------------
17  // utgb-core Project
18  //
19  // SAMLens.java
20  // Since: 2010/12/09
21  //
22  //--------------------------------------
23  package org.utgenome.format.sam;
24  
25  import java.io.File;
26  
27  import net.sf.samtools.BrowseableBAMIndex;
28  import net.sf.samtools.SAMFileReader;
29  
30  /**
31   * Lens for SAM/BAM files
32   * 
33   * @author leo
34   * 
35   */
36  public class SAMLens {
37  
38  	public static void split(File bamFile) {
39  
40  		SAMFileReader sam = new SAMFileReader(bamFile, SAMReader.getBamIndexFile(bamFile), false);
41  
42  		BrowseableBAMIndex index = sam.getBrowseableIndex();
43  
44  	}
45  
46  }