-
Notifications
You must be signed in to change notification settings - Fork 381
/
VCFtoBed.java
98 lines (80 loc) · 3.24 KB
/
VCFtoBed.java
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.variant.util;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.tribble.CodecFactory;
import htsjdk.tribble.AbstractFeatureReader;
import htsjdk.tribble.FeatureCodec;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFCodec;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.Iterator;
/**
* Utility class to convert a VCF to a BED file. Genotypes if any are lost in this converstion
*
* @author jrobinso
* @date Jan 22, 2011
*/
public class VCFtoBed {
public static void main(String[] args) throws IOException {
convert(args[0], args[1]);
}
public static void convert(String vcfFile, String bedFile) throws IOException {
AbstractFeatureReader basicReader = null;
PrintWriter writer = null;
try {
writer = new PrintWriter(new BufferedWriter(new FileWriter(bedFile)));
Genome genome = null; // Don't do alias converting
FeatureCodec codec = CodecFactory.getCodec(vcfFile, genome);
boolean isVCF = codec.getClass().isAssignableFrom(VCFCodec.class);
basicReader = AbstractFeatureReader.getFeatureReader(vcfFile, codec, true);
Iterator<VariantContext> iter = basicReader.iterator();
while (iter.hasNext()) {
VariantContext vc = iter.next();
String chr = vc.getChr();
if (!chr.startsWith("chr")) {
chr = "chr" + chr;
}
int start = vc.getStart() - 1;
int end = vc.getEnd();
String id = vc.getID();
if(id == null) {
id = ".";
}
String af = vc.getAttributeAsString("AF", "");
writer.println(chr + "\t" + start + "\t" + end + "\t" + id + "\t" + af);
}
}
finally {
if (basicReader != null)
basicReader.close();
if (writer != null)
writer.close();
}
}
}