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 // FastqToSilkReader.java
20 // Since: 2010/07/08
21 //
22 //--------------------------------------
23 package org.utgenome.format.fastq;
24
25 import java.io.IOException;
26 import java.io.Reader;
27 import java.io.Writer;
28
29 import org.utgenome.format.FormatConversionReader;
30 import org.xerial.silk.SilkWriter;
31
32 /**
33 * Read the FASTQ file input from the given reader as if it were a Silk
34 *
35 * @author leo
36 *
37 */
38 public class FastqToSilkReader extends FormatConversionReader {
39
40 public FastqToSilkReader(Reader fastqInput) throws IOException {
41 super(fastqInput, new PipeConsumer() {
42 @Override
43 public void consume(Reader in, Writer out) throws Exception {
44 FastqReader reader = new FastqReader(in);
45 SilkWriter silk = new SilkWriter(out);
46 for (FastqRead read = null; (read = reader.next()) != null;) {
47 read.toSilk(silk);
48 }
49 silk.flush();
50 }
51 });
52
53 }
54 }