--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/CompressFiles.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,71 @@
+package fileIO;
+
+import java.io.File;
+
+
+public class CompressFiles {
+	
+	
+	public static void main(String[] args){
+		for(String s : args){
+			if(s.equalsIgnoreCase("zip")){
+				zip=true;
+				gzip=false;
+			}else if(s.equalsIgnoreCase("gzip") || s.equalsIgnoreCase("gz")){
+				zip=false;
+				gzip=true;
+			}else{
+				compressFiles(s);
+			}
+		}
+	}
+	
+	
+	public static void compressFiles(String path){
+		File f=new File(path);
+		compressFiles(f);
+	}
+	
+	public static void compressFiles(File path){
+		
+		if(path.isDirectory()){
+			File[] array=path.listFiles();
+			for(File f : array){compressFiles(f);}
+		}else{
+			compress(path);
+		}
+		
+	}
+	
+	public static void compress(File in){
+		assert(in.exists());
+		assert(in.isFile());
+		String abs=in.getAbsolutePath();
+//		System.out.println("Considering "+abs);
+		if(abs.endsWith(".gz") || abs.endsWith(".zip") || abs.endsWith(".bz2")){return;}
+		
+//		if(!abs.contains("custom_summary_") || !abs.endsWith("Gene_build36.txt")){return;} //TODO ***TEMPORARY***
+		System.err.println(abs);
+//		if(!abs.endsWith(".gvla")){return;} //TODO ***TEMPORARY***
+//		if(!abs.endsWith(".gvla") ||
+//				!(abs.contains("seqGene") || abs.contains("refGene") || abs.contains("unionGene"))){return;} //TODO ***TEMPORARY***
+		if(abs.toLowerCase().contains("familytree")){return;} //TODO ***TEMPORARY***
+		
+		if(PRINT_7Z_BATCH){
+			//-mx=4 is fast; -mx=5 or 6 is slow; 7+ is very slow.
+//			System.out.println("C:"+Data.SLASH+"\"Program Files\""+Data.SLASH+"7-Zip"+Data.SLASH+"7z a -mx=4 "+abs+".zip "+abs);
+			System.out.println("C:\\\"Program Files\"\\7-Zip\\7z a -mx=4 "+abs+".gz "+abs);
+		}else{
+			System.out.println("Compressing "+abs+" to "+(zip ? "zip" : "gz"));
+			ReadWrite.copyFile(abs, abs+(zip ? ".zip" : ".gz"));
+		}
+		
+	}
+	
+	
+	public static boolean zip=true;
+	public static boolean gzip=!zip;
+	
+	public static boolean PRINT_7Z_BATCH=true;
+	
+}