ConvertPhred64toFastq33.java

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

import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintStream;
import java.util.List;

import htsjdk.samtools.fastq.FastqConstants;
import htsjdk.samtools.fastq.FastqRecord;
import htsjdk.samtools.util.CloserUtil;

import com.beust.jcommander.Parameter;
import com.github.lindenb.jvarkit.io.IOUtils;
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.FastqReader;
import com.github.lindenb.jvarkit.util.picard.FourLinesFastqReader;
import com.github.lindenb.semontology.Term;


@Program(name="fastqphred64to33",
	keywords={"fastq"},
	description="Convert Illumina Fastq 64 encoding to Fastq 33",
	terms={Term.ID_0000005}
	)
public class ConvertPhred64toFastq33 extends Launcher
	{
	private static final Logger LOG = Logger.build(ConvertPhred64toFastq33.class).make();

	@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
	private File outputFile = null;

	
	private PrintStream pw= System.out;
	private ConvertPhred64toFastq33()
		{
		
		}

	
	private void convert(InputStream in) throws IOException
		{
		FastqReader r=new FourLinesFastqReader(in);
		while(r.hasNext() && !pw.checkError())
			{
			final FastqRecord rec=r.next();
			byte quals[]=rec.getBaseQualityString().getBytes();
			for(int i=0;i< quals.length;++i )
				{
				quals[i]=(byte)(quals[i]-64+33);
				if(quals[i]<33 || quals[i]>126)
					{
					r.close();
					throw new IOException("q="+(int)quals[i]);
					}
				}
			String name=rec.getReadHeader();
			int diez=name.indexOf('#');
			if(diez!=-1) name=name.substring(0, diez);
	        pw.print(FastqConstants.SEQUENCE_HEADER);
	        pw.println(name);
	        pw.println(rec.getReadString());
	        pw.print(FastqConstants.QUALITY_HEADER);
	        pw.println(rec.getBaseQualityHeader() == null || rec.getReadHeader().equals(rec.getBaseQualityHeader())? "" : rec.getBaseQualityHeader());
	        pw.println(new String(quals));
			}
		r.close();
		}
	@Override
	public int doWork(List<String> args) {		
		try
			{
			this.pw = super.openFileOrStdoutAsPrintStream(this.outputFile);
			if(args.isEmpty())
				{
				LOG.info("Reading from stdin");
				convert(stdin());
				}
			else
				{
				for(final String filename:args)
					{
					LOG.info("Reading from "+filename);
					InputStream in=IOUtils.openURIForReading(filename);
					convert(in);
					in.close();
					}
				}
			this.pw.flush();
			this.pw.close();
			this.pw = null;
			return 0;
			}
		catch(Exception err)
			{
			LOG.error(err);
			return -1;
			}
		finally
			{
			CloserUtil.close(pw);
			}
		}
	/**
	 * @param args
	 */
	public static void main(String[] args) {
		new ConvertPhred64toFastq33().instanceMainWithExit(args);
	}

}