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package jgi;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import dna.Data;
import fileIO.PipeThread;
import fileIO.ReadWrite;
import shared.Shared;
/**
* @author Brian Bushnell
* @date Jan 22, 2013
*
*/
public class RedirectTest {
public static void main(String[] args) throws IOException{
String fin=args[0];
// String fout=args[1];
System.out.println("fin="+fin);
InputStream in=null;
final OutputStream os=System.out;
InputStream es=null;
Process p=null;
System.out.println("Samtools="+Data.SAMTOOLS());
System.out.println("Gzip="+Data.GZIP());
System.out.println("Pigz="+Data.PIGZ());
System.out.println("Gunzip="+Data.GUNZIP());
if(Shared.WINDOWS){
System.out.println("WINDOWS");
in=ReadWrite.getInputStream(fin, false, false);
}else{
System.out.println("LINUX");
p=Runtime.getRuntime().exec("gunzip -c -d "+fin);
in=p.getInputStream();
es=p.getErrorStream();
assert(es!=null);
PipeThread et=new PipeThread(es, System.err);
et.start();
System.out.println(p);
}
final byte[] buf=new byte[4096];
for(int len=in.read(buf); len>0; len=in.read(buf)){
os.write(buf, 0, len);
}
in.close();
if(es!=null){es.close();}
ReadWrite.close(os);
}
public static void main_0(String[] args) throws IOException{
String fin=args[0];
String fout=args[1];
InputStream in=ReadWrite.getInputStream(fin, false, false);
OutputStream os=System.out;
byte[] buf=new byte[4096];
for(int len=in.read(buf); len>0; len=in.read(buf)){
os.write(buf, 0, len);
}
}
}
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