--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/ByteFile.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,140 @@
+package fileIO;
+import java.io.File;
+import java.io.InputStream;
+import java.util.ArrayList;
+
+import shared.Shared;
+import structures.ListNum;
+
+
+public abstract class ByteFile {
+	
+//	public static final ByteFile makeByteFile(String fname){
+//		return makeByteFile(fname, false, true);
+//	}
+	
+	public static final ByteFile makeByteFile1(String fname, boolean allowSubprocess){
+		FileFormat ff=FileFormat.testInput(fname, FileFormat.TEXT, null, allowSubprocess, false);
+		return new ByteFile1(ff);
+	}
+	
+	public static final ByteFile makeByteFile(String fname, boolean allowSubprocess){
+		FileFormat ff=FileFormat.testInput(fname, FileFormat.TEXT, null, allowSubprocess, false);
+		return makeByteFile(ff);
+	}
+	
+	public static final ByteFile makeByteFile(FileFormat ff){
+		return makeByteFile(ff, 0);
+	}
+	
+	public static final ByteFile makeByteFile(FileFormat ff, int type){
+		if(type==1){return new ByteFile1(ff);}
+		if(type==2){return new ByteFile2(ff);}
+		if(!Shared.LOW_MEMORY && (FORCE_MODE_BF2 || (!FORCE_MODE_BF1 && Shared.threads()>4/* && (ReadWrite.isCompressed(fname) || ReadWrite.isSam(fname))*/))){
+//			if(allowSubprocess && ((ReadWrite.USE_UNPIGZ || ReadWrite.USE_GUNZIP) && (fname.endsWith(".gz") || fname.endsWith(".gzip")))){}
+			return new ByteFile2(ff);
+		}
+//		if(FORCE_MODE_BF3){return new QuickFile(ff);}
+		return new ByteFile1(ff);
+	}
+	
+	protected ByteFile(FileFormat ff_){
+		ff=ff_;
+		assert(ff.read()) : ff;
+	}
+	
+	public final ArrayList<byte[]> toByteLines(){
+		
+		byte[] s=null;
+		ArrayList<byte[]> list=new ArrayList<byte[]>(4096);
+		
+		for(s=nextLine(); s!=null; s=nextLine()){
+			list.add(s);
+		}
+		
+		return list;
+	}
+	
+	public static final ArrayList<byte[]> toLines(FileFormat ff){
+		ByteFile bf=makeByteFile(ff);
+		ArrayList<byte[]> lines=bf.toByteLines();
+		bf.close();
+		return lines;
+	}
+	
+	public static final ArrayList<byte[]> toLines(String fname){
+		FileFormat ff=FileFormat.testInput(fname, FileFormat.TEXT, null, true, false);
+		return toLines(ff);
+	}
+	
+	public final long countLines(){
+		byte[] s=null;
+		long count=0;
+		for(s=nextLine(); s!=null; s=nextLine()){count++;}
+		reset();
+		
+		return count;
+	}
+
+	public abstract void reset();
+	final void superReset(){
+		nextID=0;
+	}
+	
+	public synchronized final ListNum<byte[]> nextList(){
+		byte[] line=nextLine();
+		if(line==null){return null;}
+		ArrayList<byte[]> list=new ArrayList<byte[]>(200);
+		list.add(line);
+		for(int i=1; i<200; i++){
+			line=nextLine();
+			if(line==null){break;}
+			list.add(line);
+		}
+		ListNum<byte[]> ln=new ListNum<byte[]>(list, nextID);
+		nextID++;
+		return ln;
+	}
+	
+	public final boolean exists(){
+		return name().equals("stdin") || name().startsWith("stdin.") || name().startsWith("jar:") || new File(name()).exists(); //TODO Ugly and unsafe hack for files in jars
+	}
+
+	public abstract InputStream is();
+	public abstract long lineNum();
+	
+	/** Returns true if there was an error */
+	public abstract boolean close();
+	
+	public abstract byte[] nextLine();
+	
+//	public final void pushBack(byte[] line){
+//		assert(pushBack==null);
+//		pushBack=line;
+//	}
+	
+	public abstract void pushBack(byte[] line);
+	
+	public abstract boolean isOpen();
+	
+	public final String name(){return ff.name();}
+	public final boolean allowSubprocess(){return ff.allowSubprocess();}
+	
+	public final FileFormat ff;
+	
+	/** Force usage of ByteFile1 */
+	public static boolean FORCE_MODE_BF1=false;//!(Data.GENEPOOL || Data.DENOVO || Data.CORI || Shared.WINDOWS);
+	
+	/** Force usage of ByteFile2 */
+	public static boolean FORCE_MODE_BF2=false;
+	
+	/** Unused */
+	@Deprecated
+	public static boolean FORCE_MODE_BF3=false;
+	
+	protected final static byte slashr='\r', slashn='\n', carrot='>', plus='+', at='@';//, tab='\t';
+	
+//	byte[] pushBack=null;
+	private long nextID=0;
+	
+}