--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/gff/CompareGff.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,364 @@
+package gff;
+
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Locale;
+import java.util.Map.Entry;
+
+import fileIO.ByteFile;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import prok.ProkObject;
+import shared.Parse;
+import shared.Parser;
+import shared.PreParser;
+import shared.Shared;
+import shared.Timer;
+import shared.Tools;
+import structures.StringNum;
+
+/**
+ * Compares gff files for the purpose of grading gene-calling.
+ * @author Brian Bushnell
+ * @date October 3, 2018
+ *
+ */
+public class CompareGff {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Code entrance from the command line.
+	 * @param args Command line arguments
+	 */
+	public static void main(String[] args){
+		//Start a timer immediately upon code entrance.
+		Timer t=new Timer();
+		
+		//Create an instance of this class
+		CompareGff x=new CompareGff(args);
+		
+		//Run the object
+		x.process(t);
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+	}
+	
+	/**
+	 * Constructor.
+	 * @param args Command line arguments
+	 */
+	public CompareGff(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, getClass(), false);
+			args=pp.args;
+			outstream=pp.outstream;
+		}
+		
+		//Set shared static variables prior to parsing
+		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
+		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
+		
+		{//Parse the arguments
+			final Parser parser=parse(args);
+			overwrite=parser.overwrite;
+			append=parser.append;
+			
+			in=parser.in1;
+		}
+		
+		fixExtensions(); //Add or remove .gz or .bz2 as needed
+		checkFileExistence(); //Ensure files can be read and written
+		checkStatics(); //Adjust file-related static fields as needed for this program
+
+		ffin=FileFormat.testInput(in, FileFormat.GFF, null, true, true);
+		ffref=FileFormat.testInput(ref, FileFormat.GFF, null, true, true);
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------    Initialization Helpers    ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Parse arguments from the command line */
+	private Parser parse(String[] args){
+		
+		Parser parser=new Parser();
+		for(int i=0; i<args.length; i++){
+			String arg=args[i];
+			String[] split=arg.split("=");
+			String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+			if(b!=null && b.equalsIgnoreCase("null")){b=null;}
+
+			if(a.equals("ref")){
+				ref=b;
+			}else if(a.equals("lines")){
+				maxLines=Long.parseLong(b);
+				if(maxLines<0){maxLines=Long.MAX_VALUE;}
+			}else if(a.equals("verbose")){
+				verbose=Parse.parseBoolean(b);
+//				ByteFile1.verbose=verbose;
+//				ByteFile2.verbose=verbose;
+//				ReadWrite.verbose=verbose;
+			}else if(parser.parse(arg, a, b)){
+				//do nothing
+			}else if(i==0 && arg.indexOf('=')<0){
+				parser.in1=arg;
+			}else if(i==1 && arg.indexOf('=')<0 && ref==null){
+				ref=arg;
+			}else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+				//				throw new RuntimeException("Unknown parameter "+args[i]);
+			}
+		}
+		
+		return parser;
+	}
+	
+	/** Add or remove .gz or .bz2 as needed */
+	private void fixExtensions(){
+		in=Tools.fixExtension(in);
+		ref=Tools.fixExtension(ref);
+		if(in==null || ref==null){throw new RuntimeException("Error - at least two input files are required.");}
+	}
+	
+	/** Ensure files can be read and written */
+	private void checkFileExistence(){
+		
+		//Ensure input files can be read
+		if(!Tools.testInputFiles(true, true, in, ref)){
+			throw new RuntimeException("\nCan't read some input files.\n");  
+		}
+	}
+	
+	/** Adjust file-related static fields as needed for this program */
+	private static void checkStatics(){
+		//Adjust the number of threads for input file reading
+		if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
+			ByteFile.FORCE_MODE_BF2=true;
+		}
+		
+//		if(!ByteFile.FORCE_MODE_BF2){
+//			ByteFile.FORCE_MODE_BF2=false;
+//			ByteFile.FORCE_MODE_BF1=true;
+//		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	void process(Timer t){
+		
+		ByteFile bf=ByteFile.makeByteFile(ffin);
+		
+		processInner(bf);
+		
+		errorState|=bf.close();
+		
+		t.stop();
+		
+		outstream.println(Tools.timeLinesBytesProcessed(t, linesProcessed, bytesProcessed, 8));
+		
+		outstream.println();
+		outstream.println("Ref count:           \t"+refCount);
+		outstream.println("Query count:         \t"+queryCount);
+
+		outstream.println();
+		outstream.println("Ref-relative counts:");
+		outstream.println("True Positive Start: \t"+truePositiveStart+"\t"+(String.format(Locale.ROOT, "%.3f%%", truePositiveStart*100.0/refCount)));
+		outstream.println("True Positive Stop:  \t"+truePositiveStop+"\t"+(String.format(Locale.ROOT, "%.3f%%", truePositiveStop*100.0/refCount)));
+//		outstream.println("False Positive Start:\t"+falsePositiveStart+"\t"+(String.format(Locale.ROOT, "%.3f%%", falsePositiveStart*100.0/refCount)));
+//		outstream.println("False Positive Stop: \t"+falsePositiveStop+"\t"+(String.format(Locale.ROOT, "%.3f%%", falsePositiveStop*100.0/refCount)));
+		outstream.println("False Negative Start:\t"+falseNegativeStart+"\t"+(String.format(Locale.ROOT, "%.3f%%", falseNegativeStart*100.0/refCount)));
+		outstream.println("False Negative Stop: \t"+falseNegativeStop+"\t"+(String.format(Locale.ROOT, "%.3f%%", falseNegativeStop*100.0/refCount)));
+
+		outstream.println();
+		outstream.println("Query-relative counts:");
+		outstream.println("True Positive Start: \t"+truePositiveStart2+"\t"+(String.format(Locale.ROOT, "%.3f%%", truePositiveStart2*100.0/queryCount)));
+		outstream.println("True Positive Stop:  \t"+truePositiveStop2+"\t"+(String.format(Locale.ROOT, "%.3f%%", truePositiveStop2*100.0/queryCount)));
+		outstream.println("False Positive Start:\t"+falsePositiveStart2+"\t"+(String.format(Locale.ROOT, "%.3f%%", falsePositiveStart2*100.0/queryCount)));
+		outstream.println("False Positive Stop: \t"+falsePositiveStop2+"\t"+(String.format(Locale.ROOT, "%.3f%%", falsePositiveStop2*100.0/queryCount)));
+		
+		outstream.println();
+		outstream.println("SNR: \t"+String.format(Locale.ROOT, "%.4f", 10*Math.log10((truePositiveStart2+truePositiveStop2+0.1)/(falsePositiveStart2+falsePositiveStop2+0.1))));
+		
+		if(errorState){
+			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	@SuppressWarnings("unchecked")
+	private void processInner(ByteFile bf){
+		byte[] line=bf.nextLine();
+		
+		{
+			ArrayList<GffLine> refLines=GffLine.loadGffFile(ffref, "CDS,rRNA,tRNA", true);
+
+			refCount=refLines.size();
+			lineMap=new HashMap<StringNum, GffLine>();
+			startCountMap=new HashMap<StringNum, Integer>();
+			stopCountMap=new HashMap<StringNum, Integer>();
+			
+			for(GffLine gline : refLines){
+				final int stop=gline.trueStop();
+				StringNum sn=new StringNum(gline.seqid, stop);
+				lineMap.put(sn, gline);
+				startCountMap.put(sn, 0);
+				stopCountMap.put(sn, 0);
+				assert(lineMap.get(sn)==gline);
+//				assert(false) : "\n\nsn='"+sn+"'\n"+lineMap.containsKey(sn)+"\n"+lineMap.keySet();
+			}
+			if(verbose){
+				System.err.println(lineMap);
+				System.err.println(startCountMap);
+				System.err.println(stopCountMap);
+			}
+		}
+
+		while(line!=null){
+			if(line.length>0){
+				if(maxLines>0 && linesProcessed>=maxLines){break;}
+				linesProcessed++;
+				bytesProcessed+=(line.length+1);
+				
+				final boolean valid=(line[0]!='#');
+				if(valid){
+					queryCount++;
+					GffLine gline=new GffLine(line);
+					processLine(gline);
+				}
+			}
+			line=bf.nextLine();
+		}
+		
+		for(Entry<StringNum, Integer> e : startCountMap.entrySet()){
+			if(e.getValue()<1){
+				falseNegativeStart++;
+			}
+		}
+		for(Entry<StringNum, Integer> e : stopCountMap.entrySet()){
+			if(e.getValue()<1){
+				falseNegativeStop++;
+			}
+		}
+	}
+	
+	private void processLine(GffLine gline){
+//		boolean cds=gline.type.equals("CDS");
+//		boolean trna=gline.type.equals("tRNA");
+//		boolean rrna=gline.type.equals("rRNA");
+//		if(!cds && !trna && !rrna){return;}
+//		if(cds && !ProkObject.callCDS){return;}
+//		if(trna && !ProkObject.calltRNA){return;}
+//		if(rrna){
+//			int type=gline.prokType();
+//			if(ProkObject.processType(type)){return;}
+//		}
+		int type=gline.prokType();
+		if(!ProkObject.processType(type)){return;}
+		
+		final int stop=gline.trueStop();
+		final int start=gline.trueStart();
+		
+//		System.err.println("Considering "+start+", "+stop);
+
+		StringNum sn=new StringNum(gline.seqid, stop);
+		GffLine refline=lineMap.get(sn);
+		
+		boolean fail=(refline==null || refline.strand!=gline.strand || !refline.type.equals(gline.type));
+		if(fail){
+			if(verbose){
+				System.err.println("Can't find "+sn+"\n"+gline+"\n"+refline);
+				assert(false) : "\n\nsn='"+sn+"'\n"+lineMap.containsKey(sn)+"\n"+lineMap.keySet();
+			}
+			falsePositiveStart++;
+			falsePositiveStop++;
+			falsePositiveStart2++;
+			falsePositiveStop2++;
+		}else{
+			assert(stop==refline.trueStop());
+			truePositiveStop++;
+			truePositiveStop2++;
+			stopCountMap.put(sn, stopCountMap.get(sn)+1);
+			if(start==refline.trueStart()){
+				truePositiveStart++;
+				truePositiveStart2++;
+				startCountMap.put(sn, startCountMap.get(sn)+1);
+			}else{
+				falsePositiveStart++;
+				falsePositiveStart2++;
+			}
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	private String in=null;
+	private String ref=null;
+	
+	
+	/*--------------------------------------------------------------*/
+
+	private HashMap<StringNum, GffLine> lineMap;
+	private HashMap<StringNum, Integer> startCountMap;
+	private HashMap<StringNum, Integer> stopCountMap;
+	
+//	private HashMap<Integer, ArrayList<GffLine>> map;
+//	private HashSet<Integer> stopSet;
+//	private HashSet<Integer> startSet;
+//	private HashSet<Integer> stopSetM;
+//	private HashSet<Integer> startSetM;
+	
+	private long linesProcessed=0;
+	private long linesOut=0;
+	private long bytesProcessed=0;
+	private long bytesOut=0;
+	
+	private long maxLines=Long.MAX_VALUE;
+
+	private long falsePositiveStart=0;
+	private long falsePositiveStop=0;
+	private long truePositiveStart=0;
+	private long truePositiveStop=0;
+	private long falseNegativeStart=0;
+	private long falseNegativeStop=0;
+	
+	private long falsePositiveStart2=0;
+	private long falsePositiveStop2=0;
+	private long truePositiveStart2=0;
+	private long truePositiveStop2=0;
+	
+	private long refCount=0;
+	private long queryCount=0;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+
+	private final FileFormat ffin;
+	private final FileFormat ffref;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Common Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private PrintStream outstream=System.err;
+	public static boolean verbose=false;
+	public boolean errorState=false;
+	private boolean overwrite=false;
+	private boolean append=false;
+	
+}