--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/CompareSSU.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,514 @@
+package sketch;
+
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map.Entry;
+import java.util.concurrent.atomic.AtomicInteger;
+
+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 stream.FASTQ;
+import stream.FastaReadInputStream;
+import stream.Read;
+import structures.ByteBuilder;
+import structures.FloatList;
+import tax.TaxNode;
+import tax.TaxTree;
+import template.Accumulator;
+import template.ThreadWaiter;
+
+/**
+ * Compares SSUs, all-to-all or fractional matrix.
+ * 
+ * @author Brian Bushnell
+ * @date December 2, 2019
+ *
+ */
+public class CompareSSU implements Accumulator<CompareSSU.ProcessThread> {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        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
+		CompareSSU x=new CompareSSU(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 CompareSSU(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);
+			Parser.processQuality();
+			
+			maxReads=parser.maxReads;
+			overwrite=ReadStats.overwrite=parser.overwrite;
+			append=ReadStats.append=parser.append;
+			
+			in1=parser.in1;
+
+			out1=parser.out1;
+		}
+
+		validateParams();
+		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
+		FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
+		checkFileExistence(); //Ensure files can be read and written
+		checkStatics(); //Adjust file-related static fields as needed for this program 
+		
+		//Create output FileFormat objects
+		ffout1=FileFormat.testOutput(out1, FileFormat.TXT, null, true, overwrite, append, ordered);
+		
+		tree=(treeFile==null) ? null : TaxTree.loadTaxTree(treeFile, outstream, true, false);
+		
+		SSUMap.r16SFile=in1;
+		if(SSUMap.r16SFile!=null){
+			SSUMap.load(outstream);
+			HashMap<Integer, byte[]> ssuMap=SSUMap.r16SMap;
+			ssuList=new ArrayList<Read>(ssuMap.size());
+			for(Entry<Integer, byte[]> e : ssuMap.entrySet()){
+				int id=e.getKey();
+				byte[] value=e.getValue();
+				if(value.length>=minlen && value.length<=maxlen){
+					Read r=new Read(value, null, id);//Sets numeric ID to TaxID.
+					if(maxns<0 || r.countNocalls()<=maxns){
+						ssuList.add(r);
+					}
+				}
+			}
+			Collections.shuffle(ssuList);
+		}
+		for(int i=0; i<idLists.length; i++){
+			idLists[i]=new FloatList();
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------    Initialization Helpers    ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Parse arguments from the command line */
+	private Parser parse(String[] args){
+		
+		//Create a parser object
+		Parser parser=new Parser();
+		
+		//Set any necessary Parser defaults here
+		//parser.foo=bar;
+		
+		//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(b!=null && b.equalsIgnoreCase("null")){b=null;}
+			
+			if(a.equals("verbose")){
+				verbose=Parse.parseBoolean(b);
+			}else if(a.equals("tree")){
+				treeFile=b;
+			}else if(a.equals("ordered")){
+				ordered=Parse.parseBoolean(b);
+			}else if(a.equals("ata") || a.equals("alltoall")){
+				allToAll=Parse.parseBoolean(b);
+			}else if(a.equals("store") || a.equals("storeresults")){
+				storeResults=Parse.parseBoolean(b);
+			}else if(a.equals("minlen") || a.equals("maxlength")){
+				minlen=Parse.parseIntKMG(b);
+			}else if(a.equals("maxlen") || a.equals("maxlength")){
+				maxlen=Parse.parseIntKMG(b);
+			}else if(a.equalsIgnoreCase("maxns")){
+				maxns=Parse.parseIntKMG(b);
+			}else if(a.equals("parse_flag_goes_here")){
+				long fake_variable=Parse.parseKMG(b);
+				//Set a variable here
+			}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];
+			}
+		}
+		
+		return parser;
+	}
+	
+	/** Ensure files can be read and written */
+	private void checkFileExistence(){
+		//Ensure output files can be written
+		if(!Tools.testOutputFiles(overwrite, append, false, out1)){
+			outstream.println((out1==null)+", "+out1);
+			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output file "+out1+"\n");
+		}
+		
+		//Ensure input files can be read
+		if(!Tools.testInputFiles(false, true, in1)){
+			throw new RuntimeException("\nCan't read some input files.\n");  
+		}
+		
+		//Ensure that no file was specified multiple times
+		if(!Tools.testForDuplicateFiles(true, in1, out1)){
+			throw new RuntimeException("\nSome file names were specified multiple times.\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;
+		}
+		
+		assert(FastaReadInputStream.settingsOK());
+	}
+	
+	/** Ensure parameter ranges are within bounds and required parameters are set */
+	private boolean validateParams(){
+		return true;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Create read streams and process all data */
+	void process(Timer t){
+		
+		ByteStreamWriter bsw=makeBSW(ffout1);
+		if(bsw!=null){
+			bsw.forcePrint("#Level\tIdentity\tQueryID\tRefID\n");
+		}
+		
+		//Reset counters
+		queriesProcessed=0;
+		comparisons=0;
+		
+		//Process the reads in separate threads
+		spawnThreads(bsw);
+		
+		if(verbose){outstream.println("Finished; closing streams.");}
+		
+		//Close the read streams
+		if(bsw!=null){errorState|=bsw.poisonAndWait();}
+		
+		{
+			ByteBuilder bb=new ByteBuilder();
+			bb.append("\nLevel       \tCount\tMean"+(storeResults ? "\tMedian\t90%ile\t10%ile\tSTDev" : "")+"\n");
+			outstream.print(bb);
+			final int minlen="superkingdom".length();
+			for(int level=0; level<taxLevels; level++){
+				if(counts[level]>0){
+					bb.clear();
+					bb.append(TaxTree.levelToStringExtended(level));
+					while(bb.length()<minlen){bb.space();}
+					bb.tab().append(counts[level]).tab();
+					bb.append(sums[level]/counts[level]*100, 3);
+					if(storeResults){
+						FloatList list=idLists[level];
+						list.sort();
+						double stdev=list.stdev();
+						double median=list.median();
+//						double mode=list.mode();
+						double percent90=list.percentile(0.9f);
+						double percent10=list.percentile(0.1f);
+						bb.tab().append(median*100, 3).tab().append(percent90*100, 3).tab().append(percent10*100, 3).tab().append(stdev*100, 3);
+					}
+					bb.nl();
+					outstream.print(bb);
+				}
+			}
+		}
+		
+		//Report timing and results
+		t.stop();
+		outstream.println();
+		outstream.println(Tools.timeQueriesComparisonsProcessed(t, queriesProcessed, comparisons, 8));
+		
+		//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.");
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------       Thread Management      ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Spawn process threads */
+	private void spawnThreads(ByteStreamWriter bsw){
+		
+		//Do anything necessary prior to processing
+		
+		//Determine how many threads may be used
+		final int threads=Shared.threads();
+		
+		//Fill a list with ProcessThreads
+		ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
+		for(int i=0; i<threads; i++){
+			alpt.add(new ProcessThread(bsw, i, threads));
+		}
+		
+		//Start the threads and wait for them to finish
+		boolean success=ThreadWaiter.startAndWait(alpt, this);
+		errorState&=!success;
+		
+		//Do anything necessary after processing
+		
+	}
+	
+	@Override
+	public final void accumulate(ProcessThread pt){
+		queriesProcessed+=pt.querysProcessedT;
+		comparisons+=pt.comparisonsT;
+		errorState|=(!pt.success);
+
+		for(int i=0; i<taxLevels; i++){
+			idLists[i].addAll(pt.idListsT[i]);
+			counts[i]+=pt.countsT[i];
+			sums[i]+=pt.sumsT[i];
+		}
+	}
+	
+	@Override
+	public final boolean success(){return !errorState;}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private static ByteStreamWriter makeBSW(FileFormat ff){
+		if(ff==null){return null;}
+		ByteStreamWriter bsw=new ByteStreamWriter(ff);
+		bsw.start();
+		return bsw;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Classes        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** This class is static to prevent accidental writing to shared variables.
+	 * It is safe to remove the static modifier. */
+	class ProcessThread extends Thread {
+		
+		//Constructor
+		ProcessThread(ByteStreamWriter bsw_, final int tid_, final int threads_){
+			bsw=bsw_;
+			threadID=tid_;
+			threads=threads_;
+			listCopy=new ArrayList<Read>(ssuList.size());
+			listCopy.addAll(ssuList);
+			for(int i=0; i<idListsT.length; i++){
+				idListsT[i]=new FloatList();
+			}
+		}
+		
+		//Called by start()
+		@Override
+		public void run(){
+			//Do anything necessary prior to processing
+			
+			//Process the reads
+			processInner();
+			
+			//Do anything necessary after processing
+			
+			//Indicate successful exit status
+			success=true;
+		}
+		
+		/** Iterate through the reads */
+		void processInner(){
+			final long limit=Tools.min(ssuList.size(), (maxReads>0 ? maxReads : Integer.MAX_VALUE));
+			
+			for(int num=next.getAndIncrement(); num<limit; num=next.getAndIncrement()){
+				Read r=ssuList.get(num);
+				processRead(r);
+			}
+		}
+		
+		void processRead(Read query){
+			if(query.numericID<1){return;}//invalid TID
+			final int qid=(int)query.numericID;
+			if(tree.getNode(qid)==null) {return;}
+			if(querysProcessedT%5==0) {
+				Collections.shuffle(listCopy);
+			}
+			querysProcessedT++;
+			
+			ByteBuilder bb=new ByteBuilder();
+			
+			long seen=0;
+			for(Read ref :listCopy){
+				int rid=(int)ref.numericID;
+				if(rid!=qid && rid>0 && tree.getNode(rid)!=null){
+					int aid=tree.commonAncestor(qid, rid);
+					if(aid>0){
+						TaxNode tn=tree.getNode(aid);
+						if(tn.isRanked()){
+							int level=tn.levelExtended;
+							long mask=1L<<level;
+							if(allToAll || ((mask&printLevels)!=0 && (mask&seen)==0)){
+								seen|=mask;
+								float identity=compare(query, ref, level);
+								bb.append(TaxTree.levelToStringExtended(level)).tab().append(identity, 6);
+								bb.tab().append(qid).tab().append(rid).nl();
+							}
+						}
+					}
+				}
+			}
+			if(bsw!=null){
+				bsw.addJob(bb);
+			}
+		}
+		
+		float compare(Read query, Read ref, int level){
+			comparisonsT++;
+			float identity=SketchObject.align(query.bases, ref.bases);
+			if(storeResults){idListsT[level].add(identity);}
+			countsT[level]++;
+			sumsT[level]+=identity;
+			return identity;
+		}
+
+		/** Number of reads processed by this thread */
+		protected long querysProcessedT=0;
+		/** Number of bases processed by this thread */
+		protected long comparisonsT=0;
+		
+		/** True only if this thread has completed successfully */
+		boolean success=false;
+		
+		/** Shared output stream */
+		private final ByteStreamWriter bsw;
+		/** Thread ID */
+		final int threadID;
+		
+		final int threads;
+		
+		ArrayList<Read> listCopy;
+		
+		final FloatList[] idListsT=new FloatList[taxLevels];
+		long[] countsT=new long[taxLevels];
+		double[] sumsT=new double[taxLevels];
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary input file path */
+	private String in1=null;
+	
+	private String treeFile="auto";
+
+	/** Primary output file path */
+	private String out1=null;
+	
+	public static ArrayList<Read> ssuList=null;
+
+	final static int taxLevels=TaxTree.numTaxLevelNamesExtended;
+	static final String[] printLevelsArray=new String[] {"strain", "species", "genus", "family", "order", "class", "phylum", "superkingdom", "life"};
+	static final long printLevels=makePrintLevels(printLevelsArray);
+	
+	private final TaxTree tree;
+	
+	private static final long makePrintLevels(String[] names){
+		long mask=0;
+		for(String s : names){
+			int level=TaxTree.stringToLevelExtended(s);
+			mask|=(1L<<level);
+		}
+		return mask;
+	}
+	
+	private FloatList[] idLists=new FloatList[taxLevels];
+	private long[] counts=new long[taxLevels];
+	private double[] sums=new double[taxLevels];
+	
+	private int minlen=0;
+	private int maxlen=Integer.MAX_VALUE;
+	private int maxns=-1;
+	
+	/*--------------------------------------------------------------*/
+
+	/** Number of reads processed */
+	protected long queriesProcessed=0;
+	/** Number of bases processed */
+	protected long comparisons=0;
+
+	/** Quit after processing this many input reads; -1 means no limit */
+	private long maxReads=-1;
+	
+	private AtomicInteger next=new AtomicInteger(0);
+
+	private boolean allToAll=false;
+	private boolean storeResults=false;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Primary output file */
+	private final FileFormat ffout1;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        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;
+	/** Reads are output in input order */
+	private boolean ordered=false;
+	
+}