--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/CopyFiles.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,62 @@
+package fileIO;
+
+import java.io.File;
+
+
+public class CopyFiles {
+	
+	
+	public static void main(String[] args){
+		for(String s : args){
+			renameFiles(s);
+		}
+	}
+	
+	
+	public static void renameFiles(String path){
+		File f=new File(path);
+		renameFiles(f);
+	}
+	
+	public static void renameFiles(File path){
+		
+		if(path.isDirectory()){
+			File[] array=path.listFiles();
+			for(File f : array){renameFiles(f);}
+		}else{
+			rename(path);
+		}
+		
+	}
+	
+	public static void rename(File in){
+		assert(in.exists());
+		assert(in.isFile());
+		String abs=in.getAbsolutePath();
+		
+		
+		int dot=abs.lastIndexOf('.');
+		int slash=abs.lastIndexOf('/');
+		
+//		String[] split=Person.parsePath(abs.substring(0, slash));
+//		String name=split[0];
+//		String out=abs.substring(0, dot)+"_"+name+".txt";
+		
+		
+		
+		String fname=abs.substring(slash+1);
+		
+//		System.out.println(fname);
+		
+		
+		if(fname.startsWith("chr") && fname.endsWith(".txt")){
+			
+			String out=abs.replace(".txt", ".flow");
+			assert(!out.equals(abs)) : out+", "+abs;
+			
+			System.out.println("Renaming "+abs+" to "+out);
+			ReadWrite.copyFile(abs, out);
+		}
+	}
+	
+}