--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/clump/PivotSet.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,375 @@
+package clump;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.ArrayList;
+
+import bloom.KCountArray;
+import bloom.ReadCounter;
+import fileIO.ByteFile;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import jgi.BBMerge;
+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.FASTQ;
+import stream.FastaReadInputStream;
+import stream.Read;
+import structures.ListNum;
+
+/**
+ * Reduces reads to their feature kmer.
+ * @author Brian Bushnell
+ * @date August 19, 2016
+ *
+ */
+public class PivotSet {
+
+	/*--------------------------------------------------------------*/
+	/*----------------        Static Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Code entrance from the command line.
+	 * @param args Command line arguments
+	 */
+	public static void main(String[] args){
+		makeSet(args);
+	}
+	
+	public static KCountArray makeSet(String[] args){
+		final boolean pigz=ReadWrite.USE_PIGZ, unpigz=ReadWrite.USE_UNPIGZ;
+		Timer t=new Timer();
+		PivotSet x=new PivotSet(args);
+		KCountArray kca=x.process(t, false);
+		ReadWrite.USE_PIGZ=pigz;
+		ReadWrite.USE_UNPIGZ=unpigz;
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+		
+		return kca;
+	}
+
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Constructor.
+	 * @param args Command line arguments
+	 */
+	public PivotSet(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=KmerComparator.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("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("mincount") || a.equals("consensus")){
+				minCount=Integer.parseInt(b);
+			}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;
+			
+			in1=parser.in1;
+			in2=parser.in2;
+			
+			extin=parser.extin;
+		}
+		
+		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;
+		}
+		
+		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
+		ffin2=FileFormat.testInput(in2, FileFormat.FASTQ, extin, true, true);
+	}
+	
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+
+	private static long getCells(double fraction, int cbits){
+		final long memory=Runtime.getRuntime().maxMemory();
+		final long usable=(long)Tools.max(((memory-96000000)*.73), memory*0.45);
+		final double filterMem=usable*fraction;
+		return (long)((filterMem*8)/cbits);
+	}
+	
+	/** Create read streams and process all data */
+	public KCountArray process(Timer t, boolean amino){
+		int cbits=2;
+		while((1L<<cbits)<=minCount){cbits*=2;}
+		int filterHashes=2;
+		float fraction=0.1f;
+		long cells=getCells(fraction, cbits);
+		ReadCounter rc=new ReadCounter(k, true, ecco, false, amino);
+		KCountArray kca=rc.makeKca(null, null, null, cbits, cells, filterHashes, 0, maxReads, 1, 1, 1, 1, null, 0);
+		
+		final ConcurrentReadInputStream cris;
+		{
+			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, null, null);
+			cris.start();
+			if(verbose){outstream.println("Started cris");}
+		}
+		
+		readsProcessed=0;
+		basesProcessed=0;
+		
+		//Process the read stream
+		processInner(cris, kca);
+		
+		if(verbose){outstream.println("Finished; closing streams.");}
+		
+		errorState|=ReadStats.writeAll();
+		errorState|=ReadWrite.closeStreams(cris);
+		
+		t.stop();
+
+		outstream.println("Made filter:     \t"+kca.toShortString(filterHashes));
+		outstream.println("Estimated pivots:      \t"+(long)kca.estimateUniqueKmers(filterHashes));
+		outstream.println("Estimated pivots >1x:  \t"+(long)kca.estimateUniqueKmers(filterHashes, minCount));
+		
+		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.");
+		}
+		return kca;
+	}
+	
+	/** Manage threads */
+	public static KCountArray makeKcaStatic(final ConcurrentReadInputStream cris, int k, int minCount, boolean amino){
+
+		KmerComparator kc=new KmerComparator(k, false, false);
+		int cbits=2;
+		while((1L<<cbits)<=minCount){cbits*=2;}
+		int filterHashes=2;
+		float fraction=0.1f;
+		long cells=getCells(fraction, cbits);
+		ReadCounter rc=new ReadCounter(k, true, false, false, amino);
+		KCountArray kca=rc.makeKca(null, null, null, cbits, cells, filterHashes, 0, -1, 1, 1, 1, 1, null, 0);
+		
+		if(verbose){System.err.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, kc, kca, false));}
+		
+		if(verbose){System.err.println("Starting threads.");}
+		for(HashThread ht : alht){ht.start();}
+		
+		if(verbose){System.err.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();
+				}
+			}
+		}
+		kca.shutdown();
+		return kca;
+	}
+	
+	/** Manage threads */
+	public void processInner(final ConcurrentReadInputStream cris, KCountArray kca){
+		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, kc, kca, ecco));}
+		
+		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;
+		}
+		kca.shutdown();
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Classes        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private static class HashThread extends Thread{
+
+		HashThread(ConcurrentReadInputStream cris_, KmerComparator kc_, KCountArray kca_, boolean ecco_){
+			cris=cris_;
+			kc=kc_;
+			kca=kca_;
+			ecco=ecco_;
+		}
+
+		@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
+				for(Read r1 : reads){
+					Read r2=r1.mate;
+					readsProcessedT+=r1.pairCount();
+					basesProcessedT+=r1.pairLength();
+					if(ecco && r2!=null){
+						if(r2!=null){BBMerge.findOverlapStrict(r1, r2, true);}
+					}
+					{
+						final long kmer=kc.hash(r1, null, 0, false);
+						if(kmer>=0){
+							kca.increment(kmer);
+						}
+					}
+					if(r2!=null){
+						final long kmer=kc.hash(r2, null, 0, false);
+						if(kmer>=0){
+							kca.increment(kmer);
+						}
+					}
+				}
+				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 KmerComparator kc;
+		final KCountArray kca;
+		final boolean ecco;
+		
+		protected long readsProcessedT=0;
+		protected long basesProcessedT=0;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private int k=31;
+	private int minCount=2;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------          I/O Fields          ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private String in1=null;
+	private String in2=null;
+	
+	private String extin=null;
+	
+	/*--------------------------------------------------------------*/
+	
+	protected long readsProcessed=0;
+	protected long basesProcessed=0;
+	
+	private long maxReads=-1;
+	private boolean ecco=false;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private final FileFormat ffin1;
+	private final FileFormat ffin2;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Common Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private PrintStream outstream=System.err;
+	public static boolean verbose=false;
+	public boolean errorState=false;
+	
+}