--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fun/Calc.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,164 @@
+package fun;
+
+import java.io.PrintStream;
+import java.util.Locale;
+
+import shared.Parse;
+import shared.Parser;
+import shared.PreParser;
+import shared.ReadStats;
+import shared.Shared;
+import shared.Timer;
+
+public class Calc {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Code entrance from the command line.
+	 * @param args Command line arguments
+	 */
+	public static void main(String[] args){
+		Timer t=new Timer();
+		Calc x=new Calc(args);
+		x.process(t);
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+	}
+	
+	/**
+	 * Constructor.
+	 * @param args Command line arguments
+	 */
+	public Calc(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, getClass(), false);
+			args=pp.args;
+			outstream=pp.outstream;
+		}
+		
+		//Create a parser object
+		Parser parser=new Parser();
+		
+		//Parse each argument
+		for(int i=0; i<args.length; i++){
+			String arg=args[i];
+			
+			//Break arguments into their constituent parts, in the form of "a=b"
+			String[] split=arg.split("=");
+			String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+			
+			if(a.equals("verbose")){
+				verbose=Parse.parseBoolean(b);
+			}else if(a.equals("parse_flag_goes_here")){
+				long fake_variable=Parse.parseKMG(b);
+				//Set a variable here
+			}else if(a.equals("num") || a.equals("numstats")){
+				numStats=Integer.parseInt(b);
+			}else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
+				//do nothing
+			}else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+			}
+		}
+		
+		{//Process parser fields
+			
+			overwrite=ReadStats.overwrite=parser.overwrite;
+			append=ReadStats.append=parser.append;
+
+			out1=parser.out1;
+		}
+	}
+	
+
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Create read streams and process all data */
+	void process(Timer t){
+		
+		//Process the read stream
+		processInner(numStats);
+		
+		if(verbose){outstream.println("Finished; closing streams.");}
+		
+		//Report timing and results
+		{
+			t.stop();
+			outstream.println("Time: \t"+t);
+		}
+		
+		//Throw an exception of there was an error in a thread
+		if(errorState){
+			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
+		}
+	}
+	
+	/** Iterate through the reads */
+	void processInner(int numStats){
+		int bits=numStats*5;
+		final int iters=1<<bits;
+		final int buckets=1+31*numStats;
+		int[] counts=new int[buckets];
+		for(int i=0; i<iters; i++){
+			counts[sum(i)]++;
+		}
+		int[] cumulative=new int[buckets];
+		cumulative[0]=counts[0];
+		for(int i=1; i<buckets; i++){
+			cumulative[i]=cumulative[i-1]+counts[i];
+		}
+		//StringBuilder sb=new StringBuilder();
+		final double mult=100.0/iters;
+		for(int i=0; i<buckets; i++){
+			String s=(String.format(Locale.ROOT, "%d\t%.4f%%\n", i, cumulative[i]*mult));
+			System.out.print(s);
+		}
+	}
+	
+	int sum(int stats){
+		int sum=0;
+		while(stats>0){
+			sum+=(stats&0x1F);
+			stats>>>=5;
+		}
+		return sum;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary output file path */
+	private String out1="stdout.txt";
+	
+	private int numStats=6;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Common Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Print status messages to this output stream */
+	private PrintStream outstream=System.err;
+	/** Print verbose messages */
+	public static boolean verbose=false;
+	/** True if an error was encountered */
+	public boolean errorState=false;
+	/** Overwrite existing output files */
+	private boolean overwrite=false;
+	/** Append to existing output files */
+	private boolean append=false;
+	
+}