package mygatk;

import java.io.PrintStream;

import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

public class HelloRead extends ReadWalker<Integer, Integer>
	{
	/**
	tells the GATK that weʼre going to
	channel our output through this
	object. */
	@Output(shortName="o",fullName="output",doc="save as")
	PrintStream out;
	
	@Override
	public Integer map(ReferenceContext ref, GATKSAMRecord read,
			ReadMetaDataTracker metaDataTracker) {
		out.println(">"+read.getReadName());
		out.println(new String(read.getReadBases()));
		return null;
		}
	
	@Override
	public Integer reduceInit()
		{
		return null;
		}
	
	@Override
	public Integer reduce(Integer value, Integer sum)
		{
		return null;
		}

	}