VcfPeekVcf.java

/*
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:
* 2015 creation

*/
package com.github.lindenb.jvarkit.tools.vcfvcf;

import java.io.File;
import java.io.IOException;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import com.beust.jcommander.Parameter;
import com.github.lindenb.jvarkit.lang.JvarkitException;
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.SAMSequenceDictionaryProgress;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.CloserUtil;
import com.github.lindenb.jvarkit.util.vcf.VcfIterator;

import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.VCFFileReader;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import com.github.lindenb.jvarkit.util.vcf.VCFUtils;

@Program(name="vcfpeekvcf",
		description="Get the INFO from a VCF and use it for another VCF",
		deprecatedMsg="Use GATK or vcftools",
		keywords={"vcf"}
		)
public class VcfPeekVcf extends Launcher
	{
	private static final Logger LOG = Logger.build(VcfPeekVcf.class).make();
	
	
	@Parameter(names={"-f","--tabix"},description="The VCF file indexed with TABIX or tribble. Source of the annotations",required=true)
	private File TABIX = null;
	
	@Parameter(names={"-t","--tags"},description="tag1,tag2,tag... the INFO keys to peek from the indexed file")
	private String tagsAsString = null;
	
	@Parameter(names={"-p","--prefix"},description="prefix all database tags with this prefix to avoid collisions")
	private String peekTagPrefix = "";
	
	@Parameter(names={"-a","--alt"},description="**ALL** alt allele must be found in indexed file.")
	private boolean altAlleleCheck = false;
	
	@Parameter(names={"-i","--replaceid"},description="Replace the ID field if it exists")
	private boolean peekId = false;
	
	@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
	private File outputFile = null;

	
	private final Set<String> peek_info_tags=new HashSet<String>();
	private VCFFileReader indexedVcfFileReader=null;
	
	public VcfPeekVcf()
		{
		}
	
	
	
	/** public for knime */
	@Override
	public int doVcfToVcf(
			final String inputName, 
			final VcfIterator vcfIn,
			final VariantContextWriter out)
		{
		try
			{
			final VCFHeader h = vcfIn.getHeader();
			final VCFHeader h2 = new VCFHeader(h);
			
			super.addMetaData(h2);
			
			for(final String key: this.peek_info_tags)
				{
				VCFInfoHeaderLine hinfo =this.indexedVcfFileReader.getFileHeader().getInfoHeaderLine(key);
				if(hinfo==null)
					{
					LOG.warn("INFO name="+key+" missing in "+this.TABIX);
					continue;
					}
				hinfo = VCFUtils.renameVCFInfoHeaderLine(hinfo, this.peekTagPrefix+key);
				if(h2.getInfoHeaderLine(hinfo.getID())!=null)
					{
					throw new JvarkitException.UserError("key "+this.peekTagPrefix+key+" already defined in VCF header");
					}
				h2.addMetaDataLine(hinfo);;
				}
			
			out.writeHeader(h2);
			final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(h);
			while(vcfIn.hasNext())
				{
				final VariantContext ctx=progress.watch(vcfIn.next());
							
				final VariantContextBuilder vcb = new VariantContextBuilder(ctx);
				CloseableIterator<VariantContext> iter= this.indexedVcfFileReader.query(
						ctx.getContig(),
						Math.max(0,ctx.getStart()-1),
						(ctx.getEnd()+1)
						);
				while(iter.hasNext())
					{
					VariantContext ctx2=iter.next();
					if(!ctx.getContig().equals(ctx2.getContig())) continue;
					if(ctx.getStart()!=ctx2.getStart()) continue;
					if(!ctx.getReference().equals(ctx2.getReference())) continue;
					
					if(this.altAlleleCheck)
						{
						boolean found_all_alt=true;
						for(Allele alt: ctx.getAlternateAlleles())
							{
							if(!ctx2.hasAlternateAllele(alt))
								{
								found_all_alt=false;
								break;
								}
							}
						if(!found_all_alt) continue;
						}
					if(this.peekId && ctx2.hasID())
						{
						vcb.id(ctx2.getID());
						}
					for(final String key: this.peek_info_tags)
						{
						if(!ctx2.hasAttribute(key)) continue;
						final Object o = ctx2.getAttribute(key);
						vcb.attribute(this.peekTagPrefix+key, o);
						}
					}
				iter.close();
				iter=null;
				
				out.add(vcb.make());
					
				if(out.checkError()) break;
				}
			progress.finish();
			return 0;
			}
		catch(Exception err)
			{
			LOG.error(err);
			return -1;
			}
		}

	@Override
	public int doWork(final List<String> args) {
		this.indexedVcfFileReader = null;
		try
			{
			this.indexedVcfFileReader = new VCFFileReader(TABIX,true);
			for(final String s: this.tagsAsString.split("[, \n]+")) {
				if(s.isEmpty()) continue;
				this.peek_info_tags.add(s);
				}
			
			return doVcfToVcf(args, outputFile);
			} 
		catch(Exception err)
			{
			LOG.error(err);
			return -1;
			}
		finally
			{
			CloserUtil.close(this.indexedVcfFileReader);
			this.indexedVcfFileReader=null;
			this.peek_info_tags.clear();
			}
		}
	
	
	public static void main(String[] args) throws IOException
		{
		new VcfPeekVcf().instanceMainWithExit(args);
		}
}