VcfVcf.java

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

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Set;

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 htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.CloserUtil;
import com.github.lindenb.jvarkit.util.vcf.VcfIterator;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import com.github.lindenb.jvarkit.util.vcf.IndexedVcfFileReader;

@Deprecated
@Program(name="vcfvcf",
	description="Get the INFO from a VCF and use it for another VCF",
	deprecatedMsg="obsolete. use GATK"
	)
public class VcfVcf extends Launcher
	{
	 private static Logger LOG=Logger.build(VcfVcf.class).make(); 
	
	 @Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
	 private File outputFile = null;

	@Parameter(names="-TBX",description="The VCF file indexed with TABIX. Source of the annotations")
	public String TABIX;
	
	@Parameter(names="-INFO",description="The INFO keys to grab.")
	public Set<String> INFO_IDS=new LinkedHashSet<String>();
	
	
	
	
	@Parameter(names="-RIF",description="Replace the INFO field if it exists.")	
	public boolean REPLACE_INFO_FIELD=true;
	@Parameter(names="-RID",description="Replace the ID field if it exists.")			
	public boolean REPLACE_ID=true;
	@Parameter(names="-RAM",description="REF allele matters.")			
	public boolean REF_ALLELE_MATTERS=true;
	@Parameter(names="-AAM",description="ALT alleles matters.")			
	public boolean ALT_ALLELES_MATTERS=false;
	@Parameter(names="-ACF",description="Flag to set if alternate alleles conflict.")			
	public String ALT_CONFLICT_FLAG=null;
	
	
	@Override
	protected int doVcfToVcf(String inputName, VcfIterator r, VariantContextWriter w) {
			try
			{
			CloseableIterator<VariantContext> iter=null;
			
			LOG.info("opening file: "+this.TABIX);
		    IndexedVcfFileReader tabix= new IndexedVcfFileReader(this.TABIX);
			VCFHeader header3=tabix.getHeader();
			VCFHeader header1=r.getHeader();
			
			VCFHeader h2=new VCFHeader(header1.getMetaDataInInputOrder(),header1.getSampleNamesInOrder());
			for(String infoId:this.INFO_IDS)
				{
				VCFInfoHeaderLine vihl=header3.getInfoHeaderLine(infoId);
				if(vihl==null)
					{
					LOG.warn("Not INFO="+infoId+" in "+TABIX);
					continue;
					}
				if(h2.getInfoHeaderLine(infoId)!=null)
					{
					LOG.warn("Input already contains INFO="+vihl);
					}
				h2.addMetaDataLine(vihl);
				}
			
			if(ALT_CONFLICT_FLAG!=null)
				{
				h2.addMetaDataLine(new VCFInfoHeaderLine(ALT_CONFLICT_FLAG,1,VCFHeaderLineType.Flag,"conflict ALT allele with "+this.TABIX));
				}
			
			w.writeHeader(h2);
			while(r.hasNext())
				{
				VariantContext ctx1=r.next();
				
				VariantContextBuilder  vcb=new VariantContextBuilder(ctx1);
				String BEST_ID=null;
				boolean best_id_match_alt=false;
	
				List<VariantContext> variantsList=new ArrayList<VariantContext>();
				
			
				iter=tabix.iterator(ctx1.getChr(),
						Math.max(0,ctx1.getStart()-1),
						(ctx1.getEnd()+1)
						);
				
				while(iter.hasNext())
					{
					VariantContext ctx3=iter.next();
					if(!ctx3.getChr().equals(ctx1.getStart())) continue;
					if(ctx3.getStart()!=ctx1.getStart()) continue;
					if(ctx3.getEnd()!=ctx1.getEnd()) continue;
					
					if( ctx1.getReference().equals(ctx3.getReference()) &&
						ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles())
						)
						{
						variantsList.clear();
						variantsList.add(ctx3);
						break;
						}
					else
						{
						variantsList.add(ctx3);
						}
					}
				CloserUtil.close(iter);iter=null;
				
				for(VariantContext ctx3:variantsList)
					{
					
					
					if(this.REF_ALLELE_MATTERS && !ctx1.getReference().equals(ctx3.getReference()))
						{
						continue;
						}
					if(this.ALT_ALLELES_MATTERS && !ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles()))
						{
						continue;
						}
					
					if(ctx3.getID()!=null && this.REPLACE_ID)
						{
						if(BEST_ID!=null && best_id_match_alt)
							{
							//nothing
							}
						else
							{
							BEST_ID=ctx3.getID();
							best_id_match_alt=ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles());
							}
						}
					
					
					for(String id:this.INFO_IDS)
						{
						Object info3=ctx3.getAttribute(id);
						if(info3==null)
							{
							continue;
							}
						Object info1=ctx1.getAttribute(id);
						if(info1!=null && !this.REPLACE_INFO_FIELD)
							{
							continue;
							}
						
						vcb.attribute(id, info3);
						}
					
					if(ALT_CONFLICT_FLAG!=null && !ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles()))
						{
						vcb.attribute(ALT_CONFLICT_FLAG, true);
						}
					
					}
				if(BEST_ID!=null)
					{
					vcb.id(BEST_ID);
					}
				w.add(vcb.make());
				}
			tabix.close();
			
			return 0;
			}
		catch(Exception err) 
			{
			LOG.error(err);
			return -1;
			}
		}
	
	@Override
	public int doWork(List<String> args) {
		return doVcfToVcf(args, outputFile);
		}
	
	
	public static void main(String[] args) throws IOException
		{
		new VcfVcf().instanceMainWithExit(args);
		}
}