--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/shared/PreParser.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,204 @@
+package shared;
+
+import java.io.FileNotFoundException;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+
+import fileIO.ByteFile1;
+import json.JsonObject;
+import stream.NullOutputStream;
+
+/**
+ * Pre-parses the command line to handle:
+ * Leading hyphens
+ * Java flags
+ * Output stream redirection
+ * Help/version information
+ * 
+ * @author Brian Bushnell
+ * @date November 28, 2017
+ *
+ */
+public class PreParser {
+	
+	/**
+	 * Auxiliary constructor.
+	 * @param args Command line arguments
+	 * @param c Class object of the caller
+	 * @param printVersion True if the BBTools version should be printed to the screen
+	 */
+	public PreParser(final String[] args_, final Class<?> c, boolean printVersion){
+		this(args_, System.err, c, printVersion, true, true);
+	}
+	
+	/**
+	 * Auxiliary constructor.
+	 * @param args Command line arguments
+	 * @param defaultPrintStream Print stream that will be used if not overridden
+	 * @param c Class object of the caller
+	 * @param printVersion True if the BBTools version should be printed to the screen
+	 */
+	public PreParser(final String[] args_, PrintStream defaultPrintStream, final Class<?> c, boolean printVersion){
+		this(args_, defaultPrintStream, c, printVersion, true, true);
+	}
+	
+	/**
+	 * Primary constructor.
+	 * @param args0 Command line arguments
+	 * @param defaultPrintStream Print stream that will be used if not overridden
+	 * @param c Class object of the caller
+	 * @param printVersion True if the BBTools version should be printed to the screen
+	 * @param removeKnown Remove parameters from args that are parsed here
+	 * @param autoExit Exit if there is a version or help flag
+	 */
+	public PreParser(final String[] args0, PrintStream defaultPrintStream, final Class<?> c, boolean printVersion, boolean removeKnown, boolean autoExit){
+		original=args0;
+		if(Shared.COMMAND_LINE==null){Shared.COMMAND_LINE=(original==null ? null : original.clone());}
+		if(Shared.mainClass==null){Shared.mainClass=c;}
+		
+		Parser.parseHelp(args0, autoExit);
+		
+		String[] args=Parser.parseConfig(args0);
+		this.config=(args!=args0);
+		
+		final ArrayList<String> unknown=new ArrayList<String>(args.length);
+		int removed=0, hyphens=0;
+
+		PrintStream outstream=((defaultPrintStream == null) ? System.err : defaultPrintStream);
+		boolean help=false, jflag=false, json=false;
+		
+		for(int i=0; i<args.length; i++){
+			String s=args[i];
+			boolean remove=false;
+			if(Parser.isJavaFlag(s)){
+				jflag=true;
+				remove=true;
+			}else if(s==null){
+				remove=true;
+			}else{
+				
+//				while(a.charAt(0)=='-' && (a.indexOf('.')<0 || i>1 || !new File(a).exists())){a=a.substring(1);} //Another possibility
+				
+				if(s.length()>0 && s.charAt(0)=='-'){
+					int cnt=1;
+					while(cnt<s.length() && s.charAt(cnt)=='-'){cnt++;}
+					s=s.substring(cnt);
+					hyphens+=cnt;
+					args[i]=s;//Note that this mutates the original.  Moral:  Don't use hyphens.
+				}
+				
+				final String[] split=s.split("=");
+				assert(split.length<3) : "To many '=' signs: "+s;
+				assert(split!=null && split.length>0) : "Please do not put spaces around = symbols.\nSyntax is 'arg=value' with no spaces.";
+				final String a=split[0].toLowerCase();
+				String b=split.length>1 ? split[1] : null;
+				if(b==null){
+					//do nothing
+				}else if("null".equalsIgnoreCase(b)){//Replace "null" with nothing
+					b=null;
+					args[i]=s=(a+"=");
+				}
+				
+				if(a.equals("outstream")){
+					outstream=parseOutstream(b);
+					remove=removeKnown;
+				}else if(a.equals("json")){
+					json=Parse.parseBoolean(b);
+				}else if(a.equals("silent")){
+					silent=Parse.parseBoolean(b);
+				}else if(a.equals("printexecuting")){
+					printExecuting=Parse.parseBoolean(b);
+					remove=true;
+				}else if(a.equals("metadatafile")){
+					MetadataWriter.fnameStatic=b;
+					remove=true;
+				}else if(a.equals("bufferbf") || a.equals("bufferbf1")){//for testing
+					ByteFile1.BUFFERED=Parse.parseBoolean(b);
+					remove=true;
+				}
+			}
+			
+			if(remove){removed++;}
+			else{unknown.add(s);}
+		}
+		this.args=(removed==0 ? args : unknown.toArray(new String[0]));
+		this.outstream=outstream;
+		this.help=help;
+		this.jflag=jflag;
+		this.hyphens=hyphens;
+		this.json=json;
+		
+		if(json){
+			jsonObject=new JsonObject();
+			if(c!=null && printExecuting){jsonObject.add("commandLine", c.getName()+" "+Arrays.toString(original));}
+			if(printVersion){jsonObject.add("version", Shared.BBMAP_VERSION_STRING);}
+			jsonObject.add("memory", Shared.memTotal());
+			jsonObject.add("assertions", Shared.EA());
+			jsonObject.add("javaVersion", Shared.javaVersion);
+			jsonObject.add("JVM_args", Shared.JVM_ARGS());
+		}else if(!silent){
+			if(c!=null && printExecuting){outstream.println("Executing "+c.getName()+" "+Arrays.toString(original));}
+			if(printVersion){outstream.println("Version "+Shared.BBMAP_VERSION_STRING );}
+			if(c!=null || printVersion){outstream.println();}
+		}
+	}
+	
+	public static boolean isAmino(String[] args){
+		boolean amino=false;
+		for(String arg : args){
+			if(arg!=null && arg.startsWith("amino")){
+				final String[] split=arg.split("=");
+				assert(split.length<3) : "To many '=' signs: "+arg;
+				final String a=split[0].toLowerCase();
+				String b=split.length>1 ? split[1] : null;
+				if(a.equals("amino")){amino=Parse.parseBoolean(b);}
+			}
+		}
+		return amino;
+	}
+
+	public static int stripHyphens(String[] args){
+		int stripped=0;
+		for(int i=0; i<args.length; i++){
+			String arg=args[i];
+			if(Parser.isJavaFlag(arg)){
+				//Do nothing
+			}else if(arg.length()>0 && arg.charAt(0)=='-'){
+				int cnt=1;
+				while(cnt<arg.length() && arg.charAt(cnt)=='-'){cnt++;}
+				arg=arg.substring(cnt);
+				stripped+=cnt;
+			}
+		}
+		return stripped;
+	}
+	
+	private static PrintStream parseOutstream(final String b) {
+		
+		try {
+			if(b==null || b.equalsIgnoreCase("null")){return new PrintStream(new NullOutputStream());}
+			else if(b.equalsIgnoreCase("stdout") || b.startsWith("stdout.") || b.equals("System.out") || b.equalsIgnoreCase("sysout")){return System.out;}
+			else if(b.equalsIgnoreCase("stderr") || b.startsWith("stderr.") || b.equals("System.err")){return System.err;}
+			else{return new PrintStream(b);}
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+		}
+		KillSwitch.kill("Unable to process argument outstream="+b);
+		return null; //Unreachable
+	}
+	
+	public final String[] original;
+	public final String[] args;
+	public final PrintStream outstream;
+	public final boolean help;
+	public final boolean config;
+	public final boolean jflag;
+	public final boolean json;
+	public final int hyphens;
+	public JsonObject jsonObject; 
+
+	public static boolean printExecuting=true;
+	public static boolean silent=false;
+	
+}