--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/PipeThread.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,89 @@
+package fileIO;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+/**
+ * Listens to an output stream and copies it to an input stream.
+ * For example, redirects the error stream of some process to stderr.
+ * @author Brian Bushnell
+ * @date Jan 22, 2013
+ *
+ */
+public class PipeThread extends Thread {
+	
+//	public PipeThread(InputStream is_){this(is_, System.err);}
+	
+	public PipeThread(InputStream is_, OutputStream os_){
+		is=is_;
+		os=os_;
+		if(is==null){throw new RuntimeException("Null input stream.");}
+		if(os==null){throw new RuntimeException("Null output stream.");}
+//		synchronized(list){list.add(this);}
+	}
+	
+	@Override
+	public void run(){
+		final byte[] buf=new byte[8196];
+		try {
+			for(int len=is.read(buf); !finished && len>0; len=is.read(buf)){
+				os.write(buf, 0, len);
+			}
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		
+		if(is!=System.in){
+			try {
+				is.close();
+			} catch (IOException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+		}
+		
+		if(os!=System.out && os!=System.err){
+			ReadWrite.close(os);
+		}
+		
+		synchronized(this){
+			finished=true;
+			this.notify();
+		}
+	}
+	
+	public boolean finished(){
+		synchronized(this){
+			return finished;
+		}
+	}
+	
+	public void terminate(){
+		synchronized(this){
+			if(!finished){
+				finished=true;
+				interrupt();
+			}
+		}
+	}
+	
+//	public static void killList(){
+//		System.err.println("Kill list.");
+//		synchronized(list){
+//			for(PipeThread pt : list){
+//				if(!pt.finished){
+//					pt.terminate();
+//				}
+//			}
+//		}
+//	}
+	
+	public final InputStream is;
+	public final OutputStream os;
+	private volatile boolean finished=false;
+	
+//	private static ArrayList<PipeThread> list=new ArrayList<PipeThread>(8);
+	
+}