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package fr.inserm.umr915.tools;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.logging.Level;
import java.util.logging.Logger;


import javax.xml.XMLConstants;
import javax.xml.stream.XMLOutputFactory;
import javax.xml.stream.XMLStreamWriter;

import org.lindenb.io.IOUtils;
import org.lindenb.me.Me;

import org.lindenb.sw.vocabulary.DC;
import org.lindenb.sw.vocabulary.RDF;
import org.lindenb.sw.vocabulary.XLINK;



import fr.inserm.umr915.core.bio.vcf.VCFHeader;
import fr.inserm.umr915.core.bio.vcf.VCFRow;


public class VCFToXML
	{
	private static final Logger LOG=Logger.getLogger("fr.inserm.umr915");

	private VCFToXML()
		{
		
		}
	
	
	
	
	
	
	
	
	private void run(BufferedReader in) throws IOException
		{
		try {
			VCFHeader header=VCFHeader.read(in);
			
			XMLOutputFactory xmlfactory= XMLOutputFactory.newInstance();
			XMLStreamWriter w= xmlfactory.createXMLStreamWriter(System.out,"UTF-8");
			w.writeStartDocument("UTF-8","1.0");
			w.writeStartElement("vcf");
			w.writeAttribute("xmlns", "http://www.umr915.univ-nantes.fr/vcf/");
			w.writeAttribute("xmlns", XMLConstants.XML_NS_URI, "xlink", XLINK.NS);
			w.writeAttribute("xmlns", XMLConstants.XML_NS_URI, "rdf", RDF.NS);
			w.writeAttribute("xmlns", XMLConstants.XML_NS_URI, "dc", DC.NS);
			
			header.writeXML(w);
			
			w.writeStartElement("body");
			VCFRow row;
			
			while((row=header.nextRow(in))!=null)
				{
				row.writeXML(w);
				}
			
			w.writeEndElement();	
			
			w.writeEndElement();	
			w.writeEndDocument();
			w.flush();
			w.close();
		} catch (IOException e) {
			throw e;
			}
		catch (Exception e) {
			throw new IOException(e);
			}
		
		}
	
	public static void main(String[] args)
		{
		VCFToXML app=null;
		try {
			app=new VCFToXML();
			int optind=0;
			while(optind<args.length)
				{
				if(args[optind].equals("-h"))
					{
					System.err.println("Convert a VCF (variant call format) to XML.");
					System.err.println(Me.FIRST_NAME+" "+Me.LAST_NAME+" "+Me.WWW);
					System.err.println(" --log-level <LEVEL> optional , one of "+Level.class.getName());
					System.err.println("<file|url|stdin>");
					return;
					}
				else if(args[optind].equals("--log-level"))
					{
					LOG.setLevel(Level.parse(args[++optind]));
					}
				else if(args[optind].equals("--"))
					{
					optind++;
					break;
					}
				else if(args[optind].startsWith("-"))
					{
					System.err.println("Unnown option: "+args[optind]);
					return;
					}
				else
					{
					break;
					}
				++optind;
				}
			
			if(optind==args.length)
				{
				LOG.info("reading from stdin");
				app.run(new BufferedReader(new InputStreamReader(System.in)));
				}
			else if(optind+1==args.length)
				{
				String inputName=args[optind++];
				LOG.info("reading from "+inputName);
				BufferedReader in=IOUtils.openReader(inputName);
				app.run(in);
				in.close();
				}
			else
				{
				System.err.println("Illegal number of arguments");
				return;
				}			
			}
		catch (Exception e)
			{
			e.printStackTrace();
			}
		}
	}