/*
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.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Random;
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.samtools.util.Interval;
import htsjdk.samtools.util.IntervalTreeMap;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.VCFHeader;
import com.beust.jcommander.Parameter;
import com.github.lindenb.jvarkit.io.IOUtils;
import com.github.lindenb.jvarkit.util.bio.bed.BedLine;
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;
import com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress;
@Program(name="referencetovcf",
description="Creates a VCF containing all the possible substitutions from a Reference Genome."
)
public class ReferenceToVCF extends Launcher
{
private static final Logger LOG = Logger.build(ReferenceToVCF.class).make();
@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
private File outputFile = null;
@Parameter(names={"-L","--bed"},description="limit to this BED")
private File bedFile = null;
@Parameter(names={"-i","--insertions"},description="generate insertions")
private int insertion_size = 0;
@Parameter(names={"-d","--deletions"},description="generate deletions")
private int deletion_size = 0;
@Parameter(names={"-A","--disjoint"},description="disjoint ALT")
private boolean disjoint_alts=false;
private IntervalTreeMap<Boolean> limitBed=null;
@Override
public int doWork(List<String> args) {
if(this.bedFile!=null)
{
if(limitBed==null) limitBed=new IntervalTreeMap<Boolean>();
try
{
Pattern tab=Pattern.compile("[\t]");
BufferedReader r=IOUtils.openFileForBufferedReading(this.bedFile);
String line;
while((line=r.readLine())!=null)
{
if(BedLine.isBedHeader(line)) continue;
if(line.startsWith("#") || line.isEmpty()) continue;
String tokens[]=tab.split(line,4);
limitBed.put(new Interval(
tokens[0],
1+Integer.parseInt(tokens[1]),
1+Integer.parseInt(tokens[2])
), true);
}
CloserUtil.close(r);
}
catch(Exception err)
{
LOG.error(err);
return -1;
}
}
Random random=new Random(0L);
VariantContextWriter out=null;
try
{
IndexedFastaSequenceFile fasta=new IndexedFastaSequenceFile(new File(oneAndOnlyOneFile(args)));
SAMSequenceDictionary dict=fasta.getSequenceDictionary();
out= super.openVariantContextWriter(this.outputFile);
SAMSequenceDictionaryProgress progress=new SAMSequenceDictionaryProgress(dict);
VCFHeader header=new VCFHeader();
header.setSequenceDictionary(dict);
out.writeHeader(header);
final List<List<Allele>> combination=new ArrayList<List<Allele>>(4);
//always keep REF as first allele please
combination.add(Arrays.asList(Allele.create("A", true), Allele.create("C", false),Allele.create("G", false),Allele.create("T", false)));
combination.add(Arrays.asList(Allele.create("C", true ),Allele.create("A", false),Allele.create("G", false),Allele.create("T", false)));
combination.add(Arrays.asList(Allele.create("G", true ),Allele.create("A", false),Allele.create("C", false),Allele.create("T", false)));
combination.add(Arrays.asList(Allele.create("T", true ),Allele.create("A", false),Allele.create("C", false),Allele.create("G", false)));
for(SAMSequenceRecord ssr: dict.getSequences())
{
GenomicSequence genome=new GenomicSequence(fasta, ssr.getSequenceName());
if(this.limitBed!=null)
{
Interval interval=new Interval(ssr.getSequenceName(),1,genome.length());
if(!this.limitBed.containsOverlapping(interval) ) continue;
}
for(int n=0;n< genome.length();++n)
{
progress.watch(ssr.getSequenceIndex(), n);
List<Allele> alleles=null;
byte ref=(byte)genome.charAt(n);
switch(ref)
{
case 'a': case 'A':alleles = combination.get(0);break;
case 'c': case 'C':alleles = combination.get(1);break;
case 'g': case 'G':alleles = combination.get(2);break;
case 't': case 'T':alleles = combination.get(3);break;
default:break;
}
if(alleles==null) continue;
if(this.limitBed!=null)
{
Interval interval=new Interval(ssr.getSequenceName(), n+1, n+1);
if(!this.limitBed.containsOverlapping(interval) ) continue;
}
if(!disjoint_alts)
{
VariantContextBuilder vcb=new VariantContextBuilder();
vcb.chr(ssr.getSequenceName());
vcb.start(n+1);
vcb.stop(n+1);
vcb.alleles(alleles);
out.add(vcb.make());
}
else
{
for(int a=1;a< 4;++a)//index 0 is always REF
{
VariantContextBuilder vcb=new VariantContextBuilder();
vcb.chr(ssr.getSequenceName());
vcb.start(n+1);
vcb.stop(n+1);
vcb.alleles(Arrays.asList(alleles.get(0),alleles.get(a)));//index 0 is always REF
out.add(vcb.make());
}
}
if(insertion_size>0 &&
n+1 < genome.length() )
{
alleles=new ArrayList<Allele>(2);
//REFERENCE
alleles.add(Allele.create(""+genome.charAt(n)+genome.charAt(n+1),true));
StringBuilder sb=new StringBuilder(insertion_size+2);
sb.append(genome.charAt(n));
for(int n2=0;n2<insertion_size;++n2)
{
switch(random.nextInt(4))
{
case 0:sb.append('A');break;
case 1:sb.append('C');break;
case 2:sb.append('G');break;
case 3:sb.append('T');break;
}
}
sb.append(genome.charAt(n+1));
alleles.add(Allele.create(sb.toString(),false));
VariantContextBuilder vcb=new VariantContextBuilder();
vcb.chr(ssr.getSequenceName());
vcb.start(n+1);
vcb.alleles(alleles);
vcb.computeEndFromAlleles(alleles, n+1);
out.add(vcb.make());
}
if(deletion_size>0 &&
n+deletion_size+1 < genome.length() )
{
alleles=new ArrayList<Allele>(2);
//REF
StringBuilder sb=new StringBuilder(deletion_size+2);
sb.append(genome.charAt(n));
int lastpos=n+1;
for(int n2=0;n2<deletion_size;++n2,lastpos++)
{
sb.append(genome.charAt(lastpos));
}
sb.append(genome.charAt(lastpos));
alleles.add(Allele.create(sb.toString(),true));
alleles.add(Allele.create(""+genome.charAt(n)+genome.charAt(lastpos),false));
VariantContextBuilder vcb=new VariantContextBuilder();
vcb.chr(ssr.getSequenceName());
vcb.start(n+1);
vcb.alleles(alleles);
vcb.computeEndFromAlleles(alleles, n+1);
out.add(vcb.make());
}
if(out.checkError()) break;
}
if(out.checkError()) break;
}
progress.finish();
return 0;
}
catch(Exception err)
{
LOG.error(err);
return -1;
}
finally
{
CloserUtil.close(out);
}
}
public static void main(String[] args) {
new ReferenceToVCF().instanceMainWithExit(args);
}
}