--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/prok/RiboMaker.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,709 @@
+package prok;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.PriorityQueue;
+
+import aligner.Alignment;
+import dna.AminoAcid;
+import fileIO.ByteFile;
+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.ConcurrentReadInputStream;
+import stream.ConcurrentReadOutputStream;
+import stream.FASTQ;
+import stream.FastaReadInputStream;
+import stream.Read;
+import stream.ReadInputStream;
+import structures.ListNum;
+import structures.LongHashSet;
+import template.Accumulator;
+import template.ThreadWaiter;
+
+/**
+ * Makes a consensus ribosomal sequence using raw reads as input.
+ * 
+ * @author Brian Bushnell
+ * @date October 10, 2019
+ *
+ */
+public class RiboMaker implements Accumulator<RiboMaker.ProcessThread> {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Code entrance from the command line.
+	 * @param args Command line arguments
+	 */
+	public static void main(String[] args){
+		assert(false) : "TODO";
+		
+		//Start a timer immediately upon code entrance.
+		Timer t=new Timer();
+		
+		//Create an instance of this class
+		RiboMaker x=new RiboMaker(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 RiboMaker(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;
+			setInterleaved=parser.setInterleaved;
+			
+			in1=parser.in1;
+			in2=parser.in2;
+			qfin1=parser.qfin1;
+			qfin2=parser.qfin2;
+			extin=parser.extin;
+
+			out1=parser.out1;
+			qfout1=parser.qfout1;
+			extout=parser.extout;
+		}
+
+		validateParams();
+		doPoundReplacement(); //Replace # with 1 and 2
+		adjustInterleaving(); //Make sure interleaving agrees with number of input and output files
+		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 
+		
+		//Create output FileFormat objects
+		ffout1=FileFormat.testOutput(out1, FileFormat.FASTQ, extout, true, overwrite, append, ordered);
+		
+		fffilter=FileFormat.testInput(filterFile, FileFormat.FASTA, null, true, true);
+		ffref=FileFormat.testInput(refFile, FileFormat.FASTA, null, true, true);
+
+		//Create input FileFormat objects
+		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
+		ffin2=FileFormat.testInput(in2, FileFormat.FASTQ, extin, true, true);
+		
+		if(fffilter==null){
+			filter=null;
+		}else{
+			filter=loadFilter(fffilter, k);
+		}
+		loadRef();
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------    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("ordered")){
+				ordered=Parse.parseBoolean(b);
+			}else if(a.equals("filter")){
+				filterFile=b;
+			}else if(a.equals("ref")){
+				refFile=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;
+	}
+	
+	/** Replace # with 1 and 2 in headers */
+	private void doPoundReplacement(){
+		//Do input file # replacement
+		if(in1!=null && in2==null && in1.indexOf('#')>-1 && !new File(in1).exists()){
+			in2=in1.replace("#", "2");
+			in1=in1.replace("#", "1");
+		}
+		
+		//Ensure there is an input file
+		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
+	}
+	
+	/** Add or remove .gz or .bz2 as needed */
+	private void fixExtensions(){
+		in1=Tools.fixExtension(in1);
+		in2=Tools.fixExtension(in2);
+		qfin1=Tools.fixExtension(qfin1);
+		qfin2=Tools.fixExtension(qfin2);
+	}
+	
+	/** 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 files "+out1+"\n");
+		}
+		
+		//Ensure input files can be read
+		if(!Tools.testInputFiles(false, true, in1, in2, filterFile, refFile)){
+			throw new RuntimeException("\nCan't read some input files.\n");  
+		}
+		
+		//Ensure that no file was specified multiple times
+		if(!Tools.testForDuplicateFiles(true, in1, in2, out1, filterFile, refFile)){
+			throw new RuntimeException("\nSome file names were specified multiple times.\n");
+		}
+		
+		assert(refFile!=null);
+	}
+	
+	/** Make sure interleaving agrees with number of input and output files */
+	private void adjustInterleaving(){
+		//Adjust interleaved detection based on the number of input files
+		if(in2!=null){
+			if(FASTQ.FORCE_INTERLEAVED){outstream.println("Reset INTERLEAVED to false because paired input files were specified.");}
+			FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
+		}
+
+		//Adjust interleaved settings based on number of output files
+		if(!setInterleaved){
+			assert(in1!=null) : "\nin1="+in1+"\nin2="+in2+"\nout1="+out1+"\n";
+			if(in2!=null){ //If there are 2 input streams.
+				FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
+				outstream.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
+			}
+		}
+	}
+	
+	/** 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(){
+//		assert(minfoo>0 && minfoo<=maxfoo) : minfoo+", "+maxfoo;
+		assert(false) : "TODO";
+		return true;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Create read streams and process all data */
+	void process(Timer t){
+		
+		//Turn off read validation in the input threads to increase speed
+		final boolean vic=Read.VALIDATE_IN_CONSTRUCTOR;
+		Read.VALIDATE_IN_CONSTRUCTOR=Shared.threads()<4;
+		
+		//Create a read input stream
+		final ConcurrentReadInputStream cris=makeCris();
+		
+		//Optionally create a read output stream
+		final ConcurrentReadOutputStream ros=makeCros(cris.paired());
+		
+		//Reset counters
+		readsProcessed=readsOut=0;
+		basesProcessed=basesOut=0;
+		
+		//Process the reads in separate threads
+		spawnThreads(cris, ros);
+		
+		if(verbose){outstream.println("Finished; closing streams.");}
+		
+		//Write anything that was accumulated by ReadStats
+		errorState|=ReadStats.writeAll();
+		//Close the read streams
+		errorState|=ReadWrite.closeStreams(cris, ros);
+		
+		//Reset read validation
+		Read.VALIDATE_IN_CONSTRUCTOR=vic;
+		
+		//Report timing and results
+		t.stop();
+		outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
+		outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false));
+		
+		//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.");
+		}
+	}
+	
+	private void loadRef(){
+		ArrayList<Read> reads=ReadInputStream.toReads(ffref, -1);
+		ref0=reads.get(0).bases;
+		ref=new byte[ref0.length+2*padding];
+		for(int i=0, j=-padding; i<ref.length; i++, j++){
+			byte b=(j>=0 && j<ref0.length ? ref0[j] : (byte)'N');
+			ref[i]=b;
+		}
+		
+		queues=new PriorityQueue[1+ref.length/queueWidth];
+		for(int i=0; i<queues.length; i++){
+			queues[i]=new PriorityQueue<Alignment>(queueLen);
+		}
+	}
+	
+	public static LongHashSet loadFilter(FileFormat ff, int k){
+		if(ff==null){return null;}
+		ArrayList<Read> reads=ReadInputStream.toReads(ff, -1);
+		if(reads==null || reads.size()==0){return null;}
+		LongHashSet set=new LongHashSet(4096);
+
+		final int shift=2*k;
+		final int shift2=shift-2;
+		final long mask=(shift>63 ? -1L : ~((-1L)<<shift));
+		int len=0;
+		
+		long kmer=0, rkmer=0;
+		for(Read r : reads){
+			final byte[] bases=r.bases;
+			for(byte b : bases) {
+				long x=AminoAcid.baseToNumber[b];
+				long x2=AminoAcid.baseToComplementNumber[b];
+				kmer=((kmer<<2)|x)&mask;
+				rkmer=((rkmer>>>2)|(x2<<shift2))&mask;
+				
+				if(x>=0){
+					len++;
+					if(len>=k){
+						set.add(Tools.max(kmer, rkmer));
+					}
+				}else{
+					len=0;
+					kmer=rkmer=0;
+				}
+			}
+		}
+		return set;
+	}
+	
+	public static boolean passesFilter(Read r, int k, LongHashSet set){
+		if(r==null) {return false;}
+		if(set==null){return true;}
+
+		final int shift=2*k;
+		final int shift2=shift-2;
+		final long mask=(shift>63 ? -1L : ~((-1L)<<shift));
+		int len=0;
+		long kmer=0, rkmer=0;
+
+		final byte[] bases=r.bases;
+		for(byte b : bases) {
+			long x=AminoAcid.baseToNumber[b];
+			long x2=AminoAcid.baseToComplementNumber[b];
+			kmer=((kmer<<2)|x)&mask;
+			rkmer=((rkmer>>>2)|(x2<<shift2))&mask;
+
+			if(x>=0){
+				len++;
+				if(len>=k){
+					long key=Tools.max(kmer, rkmer);
+					if(set.contains(key)){return true;}
+				}
+			}else{
+				len=0;
+				kmer=rkmer=0;
+			}
+		}
+		return false;
+	}
+	
+	private ConcurrentReadInputStream makeCris(){
+		ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
+		cris.start(); //Start the stream
+		if(verbose){outstream.println("Started cris");}
+		boolean paired=cris.paired();
+		if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
+		return cris;
+	}
+	
+	private ConcurrentReadOutputStream makeCros(boolean pairedInput){
+		if(ffout1==null){return null;}
+
+		//Select output buffer size based on whether it needs to be ordered
+		final int buff=(ordered ? Tools.mid(16, 128, (Shared.threads()*2)/3) : 8);
+
+		final ConcurrentReadOutputStream ros=ConcurrentReadOutputStream.getStream(ffout1, null, qfout1, null, buff, null, false);
+		ros.start(); //Start the stream
+		return ros;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------       Thread Management      ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Spawn process threads */
+	private void spawnThreads(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros){
+		
+		//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(cris, i));
+		}
+		
+		//Start the threads and wait for them to finish
+		boolean success=ThreadWaiter.startAndWait(alpt, this);
+		errorState&=!success;
+		
+		//Do anything necessary after processing
+		assert(false) : "TODO: Make consensus and write it?";
+	}
+	
+	@Override
+	public final void accumulate(ProcessThread pt){
+		readsProcessed+=pt.readsProcessedT;
+		basesProcessed+=pt.basesProcessedT;
+		readsOut+=pt.readsOutT;
+		basesOut+=pt.basesOutT;
+		errorState|=(!pt.success);
+
+		for(int i=0; i<queues.length; i++){
+			PriorityQueue<Alignment> q=queues[i];
+			PriorityQueue<Alignment> qt=pt.queuesT[i];
+			for(Alignment a : qt){
+				addToQueue(a, q);
+			}
+		}
+	}
+	
+	@Override
+	public final boolean success(){return !errorState;}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	boolean addToQueue(Alignment best, PriorityQueue<Alignment>[] queues){
+		int start=best.start;
+		int qnum=start/queueWidth;
+		PriorityQueue<Alignment> queue=queues[qnum];
+		return addToQueue(best, queue);
+	}
+	
+	boolean addToQueue(Alignment best, PriorityQueue<Alignment> queue){
+		if(queue.size()<queueLen){queue.add(best);}
+		else{
+			Alignment bottom=queue.peek();
+			if(bottom.compareTo(best)>=0){return false;}
+			queue.poll();
+			queue.add(best);
+		}
+		return true;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         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(final ConcurrentReadInputStream cris_, final int tid_){
+			cris=cris_;
+			tid=tid_;
+			
+			queuesT=new PriorityQueue[1+ref.length/queueWidth];
+			for(int i=0; i<queuesT.length; i++){
+				queuesT[i]=new PriorityQueue<Alignment>(queueLen);
+			}
+		}
+		
+		//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(){
+			
+			//Grab the first ListNum of reads
+			ListNum<Read> ln=cris.nextList();
+
+			//Check to ensure pairing is as expected
+			if(ln!=null && !ln.isEmpty()){
+				Read r=ln.get(0);
+//				assert(ffin1.samOrBam() || (r.mate!=null)==cris.paired()); //Disabled due to non-static access
+			}
+
+			//As long as there is a nonempty read list...
+			while(ln!=null && ln.size()>0){
+//				if(verbose){outstream.println("Fetched "+reads.size()+" reads.");} //Disabled due to non-static access
+				
+				processList(ln);
+				
+				//Notify the input stream that the list was used
+				cris.returnList(ln);
+//				if(verbose){outstream.println("Returned a list.");} //Disabled due to non-static access
+				
+				//Fetch a new list
+				ln=cris.nextList();
+			}
+
+			//Notify the input stream that the final list was used
+			if(ln!=null){
+				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
+			}
+		}
+		
+		void processList(ListNum<Read> ln){
+
+			//Grab the actual read list from the ListNum
+			final ArrayList<Read> reads=ln.list;
+			
+			//Loop through each read in the list
+			for(int idx=0; idx<reads.size(); idx++){
+				final Read r1=reads.get(idx);
+				final Read r2=r1.mate;
+				
+				//Validate reads in worker threads
+				if(!r1.validated()){r1.validate(true);}
+				if(r2!=null && !r2.validated()){r2.validate(true);}
+
+				//Track the initial length for statistics
+				final int initialLength1=r1.length();
+				final int initialLength2=r1.mateLength();
+
+				//Increment counters
+				readsProcessedT+=r1.pairCount();
+				basesProcessedT+=initialLength1+initialLength2;
+				
+				{
+					//Reads are processed in this block.
+					processReadPair(r1, r2);
+					
+//					if(!keep){reads.set(idx, null);}
+//					else{
+//						readsOutT+=r1.pairCount();
+//						basesOutT+=r1.pairLength();
+//					}
+				}
+			}
+
+			//Output reads to the output stream
+//			if(ros!=null){ros.add(reads, ln.id);}
+		}
+		
+		/**
+		 * Process a read or a read pair.
+		 * @param r1 Read 1
+		 * @param r2 Read 2 (may be null)
+		 * @return True if the reads should be kept, false if they should be discarded.
+		 */
+		void processReadPair(final Read r1, final Read r2){
+			boolean pass=passesFilter(r1, k, filter) || passesFilter(r2, k, filter);
+			if(!pass){return;}
+			processRead(r1);
+			processRead(r2);
+		}
+		
+		void processRead(final Read r){
+			Alignment plus=new Alignment(r);
+			plus.align(ref);
+			
+			r.reverseComplement();
+			Alignment minus=new Alignment(r);
+			minus.align(ref);
+			
+			Alignment best=null;
+			if(plus.id>=minus.id){
+				r.reverseComplement();
+				best=plus;
+			}else{
+				best=minus;
+			}
+			if(best.id<minID) {return;}
+			
+			addToQueue(best, queuesT);
+		}
+
+		/** Number of reads processed by this thread */
+		protected long readsProcessedT=0;
+		/** Number of bases processed by this thread */
+		protected long basesProcessedT=0;
+		
+		/** Number of reads retained by this thread */
+		protected long readsOutT=0;
+		/** Number of bases retained by this thread */
+		protected long basesOutT=0;
+		
+		/** True only if this thread has completed successfully */
+		boolean success=false;
+		
+
+		private PriorityQueue<Alignment>[] queuesT;
+		
+		/** Shared input stream */
+		private final ConcurrentReadInputStream cris;
+		/** Thread ID */
+		final int tid;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary input file path */
+	private String in1=null;
+	/** Secondary input file path */
+	private String in2=null;
+	
+	private String qfin1=null;
+	private String qfin2=null;
+
+	/** Primary output file path */
+	private String out1=null;
+
+	private String qfout1=null;
+	
+	private String filterFile;
+	private String refFile;
+	
+	/** Override input file extension */
+	private String extin=null;
+	/** Override output file extension */
+	private String extout=null;
+	
+	/** Whether interleaved was explicitly set. */
+	private boolean setInterleaved=false;
+
+	/** Original ref */
+	private byte[] ref0;
+	/** Padded ref */
+	private byte[] ref;
+	
+	private int padding=100;
+	private int queueLen=20;
+	private int queueWidth=20;
+	private float minID=0.4f;
+	
+	private PriorityQueue<Alignment>[] queues;
+	
+	/*--------------------------------------------------------------*/
+
+	/** Number of reads processed */
+	protected long readsProcessed=0;
+	/** Number of bases processed */
+	protected long basesProcessed=0;
+
+	/** Number of reads retained */
+	protected long readsOut=0;
+	/** Number of bases retained */
+	protected long basesOut=0;
+
+	/** Quit after processing this many input reads; -1 means no limit */
+	private long maxReads=-1;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary input file */
+	private final FileFormat ffin1;
+	/** Secondary input file */
+	private final FileFormat ffin2;
+	/** Filter input file */
+	private final FileFormat fffilter;
+	/** Ref input file */
+	private final FileFormat ffref;
+	
+	/** Primary output file */
+	private final FileFormat ffout1;
+	
+	private final LongHashSet filter;
+	private final int k=31;
+	
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        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;
+	
+}