/*
The MIT License (MIT)
Copyright (c) 2014 Pierre Lindenbaum
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.
History:
* 2014 creation
*/
package com.github.lindenb.jvarkit.tools.misc;
import java.io.BufferedReader;
import java.io.File;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.regex.Pattern;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.reference.IndexedFastaSequenceFile;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.vcf.VCFStandardHeaderLines;
import com.beust.jcommander.Parameter;
import com.github.lindenb.jvarkit.util.jcommander.Launcher;
import com.github.lindenb.jvarkit.util.jcommander.Program;
import com.github.lindenb.jvarkit.util.log.Logger;
import com.github.lindenb.jvarkit.util.picard.GenomicSequence;
/**
BEGIN_DOC
### Contig conversion
chromosome 23 is converted to X or chrX, chromosome 24 is converted to Y or chrY, chromosome 25 is ignored, chromosome 26 is converted to chrM or MT.
### Example
```
$ java -jar dist/bim2vcf.jar -R human_g1k_v37.fasta input.bim
##fileformat=VCFv4.2
##INFO=<ID=MORGAN,Number=1,Type=Float,Description="Centimorgan">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Variation type">
##contig=<ID=1,length=249250621,assembly=human_g1k_v37>
(...)
#CHROM POS ID REF ALT QUAL FILTER INFO
1 12 rs73422 C . . . MORGAN=0.5224;SVTYPE=NOVARIATION
1 13 rs30315 G A . . MORGAN=0.530874;SVTYPE=SNV
1 14 rs14325 C T . . MORGAN=0.532596;SVTYPE=SNV
1 15 rs31319 A G . . MORGAN=0.532682;SVTYPE=SNV
1 16 rs954 C T . . MORGAN=0.537655;SVTYPE=SNV
1 17 rs62034 G A . . MORGAN=0.548645;SVTYPE=SNV
1 18 rs25996 A G . . MORGAN=0.575595;SVTYPE=SNV
1 19 rs12117 G A . . MORGAN=0.582608;SVTYPE=SNV
(...)
```
END_DOC
*/
@Program(name="bim2vcf",description="convert a .bim to a .vcf")
public class BimToVcf extends Launcher
{
private static final Logger LOG = Logger.build(BimToVcf.class).make();
@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
private File outputFile = null;
@Parameter(names={"-R","--reference"},description="Indexed fasta Reference",required=true)
private File REF = null;
public BimToVcf() {
}
@Override
public int doWork(List<String> args) {
VariantContextWriter w=null;
BufferedReader r=null;
IndexedFastaSequenceFile faidx=null;
GenomicSequence genomic = null;
try {
if(this.REF==null) {
LOG.error("Reference -R missing.");
return -1;
}
faidx = new IndexedFastaSequenceFile(this.REF);
final SAMSequenceDictionary dict=faidx.getSequenceDictionary();
if(dict==null) {
LOG.error("No dictionary in "+this.REF);
return -1;
}
r = super.openBufferedReader(oneFileOrNull(args));
final Set<VCFHeaderLine> headerLines = new HashSet<>();
final VCFInfoHeaderLine morgan= new VCFInfoHeaderLine("MORGAN", 1, VCFHeaderLineType.Float,"Centimorgan");
final VCFInfoHeaderLine svtype= new VCFInfoHeaderLine("SVTYPE", 1, VCFHeaderLineType.String,"Variation type");
VCFStandardHeaderLines.addStandardInfoLines(headerLines, false, "");
//super.addMetaData(headerLines);
headerLines.add(morgan);
headerLines.add(svtype);
final List<String> genotypeSampleNames = Collections.emptyList();
final VCFHeader header=new VCFHeader(headerLines, genotypeSampleNames);
header.setSequenceDictionary(dict);
w = super.openVariantContextWriter(this.outputFile);
w.writeHeader(header);
final Pattern tab=Pattern.compile("[\t]");
String line;
final Pattern iupacATGC = Pattern.compile("[atgcATGC]");
while((line=r.readLine())!=null) {
String tokens[]=tab.split(line);
if(tokens.length!=6) {
LOG.error("expected 6 column in "+line);
return -1;
}
Allele a1=null;
Allele a2=null;
Allele ref=null;
String contig=tokens[0];
SAMSequenceRecord ssr= null;
ssr = dict.getSequence(contig);
//ugly below !!
if(ssr==null && contig.equals("23"))
{
ssr = dict.getSequence("X");
}
if(ssr==null && contig.equals("23"))
{
ssr = dict.getSequence("chrX");
}
if(ssr==null && contig.equals("24"))
{
ssr = dict.getSequence("Y");
}
if(ssr==null && contig.equals("24"))
{
ssr = dict.getSequence("chrY");
}
if(ssr==null && contig.equals("26"))
{
ssr = dict.getSequence("chrM");
}
if(ssr==null && contig.equals("26"))
{
ssr = dict.getSequence("MT");
}
if(ssr==null && contig.equals("25")){
LOG.warn("ignoring "+line);
continue;
}
if(ssr==null){
LOG.error("unknown chrom in "+line);
return -1;
}
if(genomic==null || !ssr.getSequenceName().equals(genomic.getChrom())) {
genomic=new GenomicSequence(faidx, ssr.getSequenceName());
}
int pos1 = Integer.parseInt(tokens[3]);
if(tokens[4].equals("0")) tokens[4]=tokens[5];
if(tokens[5].equals("0")) tokens[5]=tokens[4];
final VariantContextBuilder vcb = new VariantContextBuilder();
vcb.chr(ssr.getSequenceName());
vcb.attribute(morgan.getID(), Float.parseFloat(tokens[2]));
if(iupacATGC.matcher(tokens[4]).matches() && iupacATGC.matcher(tokens[5]).matches())
{
String refBase=String.valueOf(genomic.charAt(pos1-1));
ref= Allele.create(refBase,true);
a1 = refBase.equalsIgnoreCase(tokens[4])?
ref:
Allele.create(tokens[4],false)
;
a2 = refBase.equalsIgnoreCase(tokens[5])?
ref:
Allele.create(tokens[5],false)
;
vcb.attribute(svtype.getID(),
a1.isReference() && a2.isReference()?
"NOVARIATION":
"SNV"
);
}
else if(
(tokens[4].equals("-") && iupacATGC.matcher(tokens[5]).matches()) ||
(tokens[5].equals("-") && iupacATGC.matcher(tokens[4]).matches())
) {
pos1--;//shift left
String refBase= String.valueOf(genomic.charAt(pos1-1));
a1 = Allele.create(refBase,false);
ref = Allele.create(refBase+tokens[tokens[4].equals("-")?5:4],true);
a2=a1;
vcb.attribute(svtype.getID(),"DEL");
}
else if(tokens[4].equals("-") && tokens[5].equals("-")) {
pos1--;//shift left
String refBase= String.valueOf(genomic.charAt(pos1-1));
a1= Allele.create(refBase,false);
ref = Allele.create(refBase+genomic.charAt(pos1),true);
a2 = a1;
vcb.attribute(svtype.getID(),"DEL");
}
else
{
LOG.error("not handled: "+line);
return -1;
}
final Set<Allele> alleles = new HashSet<>();
alleles.add(ref);
alleles.add(a1);
alleles.add(a2);
vcb.start(pos1);
vcb.stop(pos1+ref.length()-1);
if(!tokens[1].isEmpty()) vcb.id(tokens[1]);
vcb.alleles(alleles);
w.add(vcb.make());
}
r.close();r=null;
w.close();w=null;
return RETURN_OK;
} catch (Exception e) {
LOG.error(e);
return -1;
} finally {
CloserUtil.close(faidx);
CloserUtil.close(w);
CloserUtil.close(r);
}
}
public static void main(String[] args) {
new BimToVcf().instanceMainWithExit(args);
}
}