--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/clump/KmerReduce.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,413 @@
+package clump;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Random;
+
+import assemble.AbstractRemoveThread;
+import dna.AminoAcid;
+import fileIO.ByteFile;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import jgi.BBMerge;
+import kmer.KmerTableSet;
+import shared.KillSwitch;
+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 structures.ListNum;
+
+/**
+ * Reduces reads to their feature kmer.
+ * @author Brian Bushnell
+ * @date Nov 10, 2015
+ *
+ */
+public class KmerReduce {
+
+	/*--------------------------------------------------------------*/
+	/*----------------        Static Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Code entrance from the command line.
+	 * @param args Command line arguments
+	 */
+	public static void main(String[] args){
+		final boolean pigz=ReadWrite.USE_PIGZ, unpigz=ReadWrite.USE_UNPIGZ;
+		Timer t=new Timer();
+		KmerReduce x=new KmerReduce(args);
+		x.process(t);
+		ReadWrite.USE_PIGZ=pigz;
+		ReadWrite.USE_UNPIGZ=unpigz;
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+	}
+	
+	/**
+	 * @param fname0 Input filename of reads
+	 * @param k Kmer length
+	 * @param cutoff Minimum count to retain
+	 * @return Set of pivot kmers
+	 */
+	public static KmerTableSet getValidKmersFromReads(final String fname0, int k, int cutoff){
+		final String fname=fname0+"_"+(new Random().nextLong()>>>1)+".fa.gz";
+		assert(!new File(fname).exists());
+
+		ArrayList<String> arglist=new ArrayList<String>();
+		arglist.add("in="+fname0);
+		arglist.add("out="+fname);
+		arglist.add("k="+k);
+		String[] args=arglist.toArray(new String[0]);
+
+		main(args);
+
+		assert(false) : fname+", "+k+", "+cutoff;
+		KmerTableSet set=getValidKmers(fname, k, cutoff);
+		File f=new File(fname);
+		if(f.exists()){f.delete();}
+		
+		return set;
+	}
+	
+	/**
+	 * @param fname Input filename of pivot kmers
+	 * @param k Kmer length
+	 * @param cutoff Minimum count to retain
+	 * @return Set of pivot kmers
+	 */
+	public static KmerTableSet getValidKmers(final String fname, int k, int cutoff){
+		ArrayList<String> arglist=new ArrayList<String>();
+		arglist.add("in="+fname);
+		arglist.add("k="+k);
+		if(cutoff>1 && prefilter){
+			arglist.add("prefilter="+(cutoff-1));
+		}
+		
+		String[] args=arglist.toArray(new String[0]);
+		KmerTableSet set=new KmerTableSet(args, 12);
+		
+		Timer t=new Timer();
+		
+		set.process(t);
+//		errorState|=set.errorState;
+		assert(!set.errorState);
+		t.stop();
+		
+		set.prefilterArray=null;
+		AbstractRemoveThread.process(Shared.threads(), cutoff, Integer.MAX_VALUE, set, true);
+		
+		return set;
+	}
+
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Constructor.
+	 * @param args Command line arguments
+	 */
+	public KmerReduce(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, getClass(), false);
+			args=pp.args;
+			outstream=pp.outstream;
+		}
+		
+		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
+		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
+		
+		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(parser.parse(arg, a, b)){
+				//do nothing
+			}else if(a.equals("verbose")){
+				verbose=Parse.parseBoolean(b);
+			}else if(a.equals("parse_flag_goes_here")){
+				//Set a variable here
+			}else if(a.equals("k")){
+				k=Integer.parseInt(b);
+				assert(k>0 && k<32);
+			}else if(a.equals("comparisons") || a.equals("c")){
+				//do nothing
+			}else if(a.equals("ecco")){
+				ecco=Parse.parseBoolean(b);
+			}else if(a.equals("rename") || a.equals("addname")){
+				//do nothing
+			}else if(a.equals("rcomp") || a.equals("reversecomplement")){
+				//do nothing
+			}else if(a.equals("condense") || a.equals("consensus")){
+				//do nothing
+			}else if(a.equals("correct") || a.equals("ecc")){
+				//do nothing
+			}else if(a.equals("groups") || a.equals("g") || a.equals("sets") || a.equals("ways")){
+				//do nothing
+			}else if(a.equals("seed")){
+				KmerComparator.defaultSeed=Long.parseLong(b);
+			}else if(a.equals("hashes")){
+				KmerComparator.setHashes(Integer.parseInt(b));
+			}else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+				//				throw new RuntimeException("Unknown parameter "+args[i]);
+			}
+		}
+		
+		{//Process parser fields
+			Parser.processQuality();
+			
+			maxReads=parser.maxReads;
+			
+			overwrite=ReadStats.overwrite=parser.overwrite;
+			append=ReadStats.append=parser.append;
+			
+			in1=parser.in1;
+			in2=parser.in2;
+
+			out1=parser.out1;
+			
+			extin=parser.extin;
+			extout=parser.extout;
+		}
+		
+		if(in1!=null && in2==null && in1.indexOf('#')>-1 && !new File(in1).exists()){
+			in2=in1.replace("#", "2");
+			in1=in1.replace("#", "1");
+		}
+		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;
+		}
+		
+		assert(FastaReadInputStream.settingsOK());
+		
+		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
+		
+		if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
+			ByteFile.FORCE_MODE_BF2=true;
+		}
+
+		if(out1!=null && out1.equalsIgnoreCase("null")){out1=null;}
+		
+		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");
+		}
+		
+		ffout1=FileFormat.testOutput(out1, FileFormat.FASTQ, extout, true, overwrite, append, false);
+		
+		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
+		ffin2=FileFormat.testInput(in2, FileFormat.FASTQ, extin, true, true);
+	}
+	
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Create read streams and process all data */
+	void process(Timer t){
+		
+		final ConcurrentReadInputStream cris;
+		{
+			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, null, null);
+			cris.start();
+			if(verbose){outstream.println("Started cris");}
+		}
+		boolean paired=cris.paired();
+		
+		final ConcurrentReadOutputStream ros;
+		if(out1!=null){
+			final int buff=Tools.max(4, Shared.threads());
+
+			assert(!out1.equalsIgnoreCase(in1) && !out1.equalsIgnoreCase(in1)) : "Input file and output file have same name.";
+			
+			ros=ConcurrentReadOutputStream.getStream(ffout1, null, buff, null, false);
+			ros.start();
+		}else{ros=null;}
+		
+		readsProcessed=0;
+		basesProcessed=0;
+		
+		//Process the read stream
+		processInner(cris, ros);
+		
+		if(verbose){outstream.println("Finished; closing streams.");}
+		
+		errorState|=ReadStats.writeAll();
+		errorState|=ReadWrite.closeStreams(cris, ros);
+		
+		t.stop();
+		
+		outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
+		
+		if(errorState){
+			Clumpify.sharedErrorState=true;
+			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
+		}
+	}
+	
+	/** Manage threads */
+	public void processInner(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros){
+		if(verbose){outstream.println("Making comparator.");}
+		KmerComparator kc=new KmerComparator(k, false, false);
+		
+		if(verbose){outstream.println("Making hash threads.");}
+		final int threads=Shared.threads();
+		ArrayList<HashThread> alht=new ArrayList<HashThread>(threads);
+		for(int i=0; i<threads; i++){alht.add(new HashThread(cris, ros, kc));}
+		
+		if(verbose){outstream.println("Starting threads.");}
+		for(HashThread ht : alht){ht.start();}
+		
+		if(verbose){outstream.println("Waiting for threads.");}
+		/* Wait for threads to die */
+		for(HashThread ht : alht){
+			
+			/* Wait for a thread to die */
+			while(ht.getState()!=Thread.State.TERMINATED){
+				try {
+					ht.join();
+				} catch (InterruptedException e) {
+					e.printStackTrace();
+				}
+			}
+			readsProcessed+=ht.readsProcessedT;
+			basesProcessed+=ht.basesProcessedT;
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Classes        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private class HashThread extends Thread{
+
+		HashThread(ConcurrentReadInputStream cris_, ConcurrentReadOutputStream ros_, KmerComparator kc_){
+			cris=cris_;
+			ros=ros_;
+			kc=kc_;
+		}
+
+		@Override
+		public void run(){
+			
+			ListNum<Read> ln=cris.nextList();
+			ArrayList<Read> reads=(ln!=null ? ln.list : null);
+			
+			while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
+				ArrayList<Read> out=new ArrayList<Read>(reads.size());
+				for(Read r : reads){
+					if(ecco && r.mate!=null){
+						if(r.mate!=null){BBMerge.findOverlapStrict(r, r.mate, true);}
+					}
+					final long kmer=kc.hash(r, null, 0, false);
+					readsProcessedT++;
+					basesProcessedT+=r.length();
+					if(kmer>=0){
+						Read temp=new Read(toBytes(kmer), null, header, r.numericID);
+						out.add(temp);
+					}
+				}
+				if(ros!=null){ros.add(out, ln.id);}
+				cris.returnList(ln);
+				ln=cris.nextList();
+				reads=(ln!=null ? ln.list : null);
+			}
+			if(ln!=null){
+				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
+			}
+		}
+		
+		final ConcurrentReadInputStream cris;
+		final ConcurrentReadOutputStream ros;
+		final KmerComparator kc;
+		
+		protected long readsProcessedT=0;
+		protected long basesProcessedT=0;
+		
+		private static final String header="1";
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public byte[] toBytes(final long kmer){
+		byte[] dest=KillSwitch.allocByte1D(k);
+		fill(kmer, dest, 0);
+		return dest;
+	}
+	
+	public void fill(final long kmer, final byte[] dest, int pos){
+		for(int i=k-1; i>=0; i--, pos++){
+			int x=(int)((kmer>>(2*i))&3);
+			dest[pos]=AminoAcid.numberToBase[x];
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private int k=31;
+	static boolean prefilter=true;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------          I/O Fields          ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private String in1=null;
+	private String in2=null;
+	
+	private String out1=null;
+	
+	private String extin=null;
+	private String extout=null;
+	
+	/*--------------------------------------------------------------*/
+	
+	protected long readsProcessed=0;
+	protected long basesProcessed=0;
+	
+	private long maxReads=-1;
+	protected boolean ecco=false;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private final FileFormat ffin1;
+	private final FileFormat ffin2;
+
+	private final FileFormat ffout1;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Common Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private PrintStream outstream=System.err;
+	public static boolean verbose=false;
+	public boolean errorState=false;
+	private boolean overwrite=false;
+	private boolean append=false;
+	
+}