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 }