--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/MergeSketch.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,321 @@
+package sketch;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import fileIO.ByteFile;
+import fileIO.ByteStreamWriter;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import shared.Parse;
+import shared.Parser;
+import shared.PreParser;
+import shared.ReadStats;
+import shared.Shared;
+import shared.Timer;
+import shared.Tools;
+import structures.ByteBuilder;
+
+/**
+ * Combines multiple sketches into a single sketch.
+ * 
+ * @author Brian Bushnell
+ * @date July 23, 2018
+ *
+ */
+public class MergeSketch extends SketchObject {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        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();
+		
+		final boolean oldUnpigz=ReadWrite.USE_UNPIGZ;
+		final int oldBufLen=Shared.bufferLen();
+		
+		//Create an instance of this class
+		MergeSketch x=new MergeSketch(args);
+		
+		//Run the object
+		x.process(t);
+		
+		ReadWrite.USE_UNPIGZ=oldUnpigz;
+		Shared.setBufferLen(oldBufLen);
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+		
+		assert(!x.errorState) : "This program ended in an error state.";
+	}
+	
+	/**
+	 * Constructor.
+	 * @param args Command line arguments
+	 */
+	public MergeSketch(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, null, false);
+			args=pp.args;
+			outstream=pp.outstream;
+		}
+		
+		//Set shared static variables
+		ReadWrite.USE_UNPIGZ=true;
+		KILL_OK=true;
+		
+		//Create a parser object
+		Parser parser=new Parser();
+		parser.out1="stdout.txt";
+		
+		defaultParams.printRefFileName=true;
+		
+		//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("in")){
+				addFiles(b, in);
+			}else if(parseSketchFlags(arg, a, b)){
+				//Do nothing
+			}else if(defaultParams.parse(arg, a, b)){
+				//Do nothing
+			}
+//			else if(a.equals("size")){
+//				size=Parse.parseIntKMG(b);
+//			}
+			
+			else if(a.equals("parse_flag_goes_here")){
+				long fake_variable=Parse.parseKMG(b);
+				//Set a variable here
+			}
+			
+			else if(a.equals("name") || a.equals("taxname")){
+				outTaxName=b;
+			}else if(a.equals("name0")){
+				outName0=b;
+			}else if(a.equals("fname")){
+				outFname=b;
+			}else if(a.equals("taxid") || a.equals("tid")){
+				outTaxID=Integer.parseInt(b);
+			}else if(a.equals("spid")){
+				outSpid=Integer.parseInt(b);
+			}else if(a.equals("imgid")){
+				outImgID=Integer.parseInt(b);
+			}else if((a.startsWith("meta_") || a.startsWith("mt_")) && b!=null){
+				if(outMeta==null){outMeta=new ArrayList<String>();}
+				int underscore=a.indexOf('_', 0);
+				outMeta.add(a.substring(underscore+1)+":"+b);
+			}
+			
+			else if(a.equals("out") || a.equals("outsketch") || a.equals("outs") || a.equals("sketchout") || a.equals("sketch")){
+				outSketch=b;
+			}
+			
+			else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
+				//do nothing
+			}
+			
+			else if(b==null && new File(arg).exists()){
+				in.add(arg);
+			}
+			
+			else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+			}
+		}
+		outMeta=SketchObject.fixMeta(outMeta);
+		
+		blacklist=null;
+		
+		postParse();
+		
+		{//Process parser fields
+			overwrite=ReadStats.overwrite=parser.overwrite;
+			append=ReadStats.append=parser.append;
+		}
+		
+		//Ensure there is an input file
+		if(in.isEmpty()){throw new RuntimeException("Error - at least one input file is required.");}
+		
+		//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;
+		}
+		
+		ffout=FileFormat.testOutput(outSketch, FileFormat.SKETCH, null, false, overwrite, append, false);
+		if(ffout!=null && !ffout.stdio() && !defaultParams.setColors){defaultParams.printColors=false;}
+		
+		if(!Tools.testOutputFiles(overwrite, append, false, outSketch)){
+			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output file "+outSketch+"\n");
+		}
+		
+		//Ensure that no file was specified multiple times
+		if(!Tools.testForDuplicateFiles(true, in.toArray(new String[0]))){
+			throw new RuntimeException("\nSome file names were specified multiple times.\n");
+		}
+		
+		tool=new SketchTool(targetSketchSize, defaultParams);
+		
+//		assert(false) : defaultParams.toString()+"\n"+k+", "+amino+", "+HASH_VERSION;
+		if(verbose){
+			if(useWhitelist){outstream.println("Using a whitelist.");}
+			if(blacklist!=null){outstream.println("Using a blacklist.");}
+		}
+		
+		defaultParams.postParse(false, false);
+		allowMultithreadedFastq=(in.size()==1 && Shared.threads()>2);
+		if(!allowMultithreadedFastq){Shared.capBufferLen(40);}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private void process(Timer t){
+		Timer ttotal=new Timer();
+		
+		t.start();
+		inSketches=tool.loadSketches_MT(defaultParams, in);
+		final int numLoaded=(inSketches.size());
+		long sum=0;
+		for(Sketch sk : inSketches){
+			sum+=sk.length();
+		}
+		t.stop();
+		outstream.println("Loaded "+numLoaded+" sketch"+(numLoaded==1 ? "" : "es")+" of total size "+sum+" in "+t);
+		t.start();
+//		outstream.println(inSketches.get(0));
+		
+		ByteBuilder bb=new ByteBuilder();
+		
+		int sizeOut=(int)(Sketch.AUTOSIZE ? sum : Tools.min(Sketch.targetSketchSize, sum));
+		{
+			Sketch.AUTOSIZE=false;
+			Sketch.targetSketchSize=sizeOut;
+			Sketch.maxGenomeFraction=1;
+		}
+		SketchHeap heap=new SketchHeap(sizeOut, 0, tool.trackCounts);
+		for(Sketch sk : inSketches){
+			heap.add(sk);
+		}
+		heap.genomeSizeKmers=Tools.max(heap.genomeSizeKmers, sizeOut);
+		ArrayList<String> meta=inSketches.get(0).meta;
+		if(meta==null){meta=outMeta;}
+		else if(outMeta!=null){meta.addAll(outMeta);}
+		Sketch union=new Sketch(heap, false, tool.trackCounts, outMeta);
+
+		if(outTaxName!=null){union.setTaxName(outTaxName);}
+		if(outFname!=null){union.setFname(outFname);}
+		if(outName0!=null){union.setName0(outName0);}
+
+		if(outTaxID>=0){union.taxID=(outTaxID);}
+		if(outSpid>=0){union.spid=(outSpid);}
+		if(outImgID>=0){union.imgID=(outImgID);}
+		
+		if(outSketch!=null){
+			ByteStreamWriter bsw=new ByteStreamWriter(outSketch, overwrite, append, true, FileFormat.SKETCH);
+			bsw.start();
+			union.toBytes(bb);
+			bsw.print(bb);
+			bb.clear();
+			bsw.poisonAndWait();
+			errorState|=bsw.errorState;
+			t.stop();
+			outstream.println("Wrote "+1+" sketch of total size "+union.length()+" in \t"+t);
+		}
+		
+		t.stop();
+//		outstream.println("\nRan "+(inSketches.size()*refSketches.size())+" comparisons in \t"+t);
+		ttotal.stop();
+		outstream.println("Total Time: \t"+ttotal);
+	}
+	
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private static boolean addFiles(String a, Collection<String> list){
+		int initial=list.size();
+		if(a==null){return false;}
+		File f=null;
+		if(a.indexOf(',')>=0){f=new File(a);}
+		if(f==null || f.exists()){
+			list.add(a);
+		}else{
+			for(String s : a.split(",")){
+				list.add(s);
+			}
+		}
+		return list.size()>initial;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private ArrayList<String> in=new ArrayList<String>();
+	
+	private String outSketch=null;
+	
+	private final SketchTool tool;
+	
+	private ArrayList<Sketch> inSketches;
+	
+	/*Override metadata */
+	private String outTaxName=null;
+	private String outFname=null;
+	private String outName0=null;
+	private int outTaxID=-1;
+	private long outSpid=-1;
+	private long outImgID=-1;
+	private ArrayList<String> outMeta=null;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary output file */
+	private final FileFormat ffout;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        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;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Static Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Don't print caught exceptions */
+	public static boolean suppressErrors=false;
+	
+}