--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/prok/MergeRibo.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,732 @@
+package prok;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.Map.Entry;
+import java.util.concurrent.ConcurrentLinkedQueue;
+
+import aligner.SingleStateAlignerFlat2;
+import consensus.BaseGraph;
+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 structures.IntHashSet;
+import structures.ListNum;
+import tax.GiToTaxid;
+import template.Accumulator;
+import template.ThreadWaiter;
+
+/**
+ * Picks one ribosomal (16S) sequence per taxID.
+ * 
+ * @author Brian Bushnell
+ * @date November 19, 2015
+ *
+ */
+public class MergeRibo implements Accumulator<MergeRibo.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
+		MergeRibo x=new MergeRibo(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 MergeRibo(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();
+//		Shared.capBufferLen(40);//This does not help; the slowness comes from unevenness in list length during pickBest.
+		//To fix it, long lists should be sorted to be first.
+		
+		BaseGraph.MAF_sub=0.251f;
+		BaseGraph.MAF_del=0.0f;
+		BaseGraph.MAF_ins=0.0f;
+		BaseGraph.MAF_noref=0.0f;
+		BaseGraph.trimDepthFraction=0.3f;
+		BaseGraph.trimNs=true;
+		
+		{//Parse the arguments
+			final Parser parser=parse(args);
+			Parser.processQuality();
+			
+			maxReads=parser.maxReads;
+			overwrite=ReadStats.overwrite=parser.overwrite;
+			append=ReadStats.append=parser.append;
+			
+			extin=parser.extin;
+
+			out1=parser.out1;
+			extout=parser.extout;
+		}
+
+		validateParams();
+		adjustInterleaving(); //Make sure interleaving agrees with number of input and output files
+		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.FASTA, extout, true, overwrite, append, ordered);
+
+		//Create input FileFormat objects
+		ffin=new ArrayList<FileFormat>(in.size());
+		ffalt=FileFormat.testInput(alt, FileFormat.FASTA, extin, true, true);
+		for(String s : in){
+			FileFormat ff=FileFormat.testInput(s, FileFormat.FASTA, extin, true, true);
+			ffin.add(ff);
+		}
+		
+		//Determine how many threads may be used
+		threads=Shared.threads();
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------    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("consensus")){
+				useConsensus=Parse.parseBoolean(b);
+			}else if(a.equals("best")){
+				useConsensus=!Parse.parseBoolean(b);
+			}else if(a.equals("fast")){
+				fast=Parse.parseBoolean(b);
+			}else if(a.equals("minid")){
+				minID=Float.parseFloat(b);
+			}else if(a.equals("maxns")){
+				maxns=Integer.parseInt(b);
+			}else if(a.equals("minlen")){
+				minlen=Integer.parseInt(b);
+			}else if(a.equals("maxlen")){
+				maxlen=Integer.parseInt(b);
+			}else if(a.equals("in")){
+				Tools.addFiles(b, in);
+			}else if(a.equals("alt")){
+				alt=b;
+			}else if(a.equalsIgnoreCase("process16S") || a.equalsIgnoreCase("16S")){
+				process16S=Parse.parseBoolean(b);
+				process18S=!process16S;
+			}else if(a.equalsIgnoreCase("process18S") || a.equalsIgnoreCase("18S")){
+				process18S=Parse.parseBoolean(b);
+				process16S=!process18S;
+			}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 if(b==null && new File(arg).exists()){
+				in.add(arg);
+			}else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+			}
+		}
+		assert(!in.isEmpty()) : "No input file.";
+		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 files "+out1+"\n");
+		}
+		
+		//Ensure input files can be read
+		if(!Tools.testInputFiles(false, true, in)){
+			throw new RuntimeException("\nCan't read some input files.\n");  
+		}
+		
+//		//Ensure that no file was specified multiple times
+//		if(!Tools.testForDuplicateFiles(true, out1, in.toArray(new String[0]))){
+//			throw new RuntimeException("\nSome file names were specified multiple times.\n");
+//		}
+	}
+	
+	/** Make sure interleaving agrees with number of input and output files */
+	private void adjustInterleaving(){
+		FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
+	}
+	
+	/** 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";
+		assert(process16S || process18S) : "16S or 18S must be selected.";
+		assert(!process16S || !process18S) : "16S or 18S are both selected; only one may be active.";
+		return true;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Create read streams and process all data */
+	void process(Timer t){
+
+		if(process16S){
+			Read[] data=ProkObject.loadConsensusSequenceType("16S", true, true);
+			consensus16S=data[0].bases;
+			if(verbose){System.err.println("process16S: Loaded 16S consensus, length "+consensus16S.length+": "+new String(consensus16S));}
+		}
+		if(process18S){
+			Read[] data=ProkObject.loadConsensusSequenceType("18S", true, true);
+			consensus18S=data[0].bases;
+			if(verbose){System.err.println("process18S: Loaded 18S consensus, length "+consensus18S.length+": "+new String(consensus18S));}
+		}
+		
+		//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;
+		
+		//Reset counters
+		readsProcessed=readsOut=0;
+		basesProcessed=basesOut=0;
+		
+		//Align everything to global consensus
+		for(FileFormat ff : ffin) {
+			//Create a read input stream
+			final ConcurrentReadInputStream cris=makeCris(ff);
+
+			//Process the reads in separate threads
+			spawnThreads(cris, false);
+			errorState|=ReadWrite.closeStream(cris);
+		}
+		
+		if(ffalt!=null){
+			//Create a read input stream
+			final ConcurrentReadInputStream cris=makeCris(ffalt);
+
+			//Process the reads in separate threads
+			spawnThreads(cris, true);
+			errorState|=ReadWrite.closeStream(cris);
+		}
+		
+//		queue=new ConcurrentLinkedQueue<ArrayList<Ribo>>();
+//		for(Entry<Integer, ArrayList<Ribo>> e : listMap.entrySet()){
+//			queue.add(e.getValue());
+//		}
+//		listMap=null;
+		queue=makeQueue();
+		
+		//Run a second pass to pick the best SSU per taxID
+		spawnThreads(null, false);
+		
+		//Do anything necessary after processing
+		if(ffout1!=null){
+			//Optionally create a read output stream
+			final ConcurrentReadOutputStream ros=makeCros();
+			long num=0;
+			for(Ribo ribo : bestList){
+				Read r=ribo.r;
+				readsOut++;
+				basesOut+=r.length();
+				ArrayList<Read> list=new ArrayList<Read>(1);
+				list.add(r);
+				ros.add(list, num);
+				num++;
+			}
+			//Close the read streams
+			errorState|=ReadWrite.closeStream(ros);
+		}
+		
+		if(verbose){outstream.println("Finished; closing streams.");}
+		
+		//Write anything that was accumulated by ReadStats
+		errorState|=ReadStats.writeAll();
+		
+		//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 ConcurrentLinkedQueue<ArrayList<Ribo>> makeQueue(){
+		ArrayList<ArrayList<Ribo>> listList=new ArrayList<ArrayList<Ribo>>(listMap.size());
+		for(Entry<Integer, ArrayList<Ribo>> e : listMap.entrySet()){
+			listList.add(e.getValue());
+		}
+		listMap=null;
+		Collections.sort(listList, new ListComparator());
+		assert(listList.isEmpty() || listList.get(0).size()>=listList.get(listList.size()-1).size());
+		ConcurrentLinkedQueue<ArrayList<Ribo>> q=new ConcurrentLinkedQueue<ArrayList<Ribo>>();
+		for(ArrayList<Ribo> x : listList){
+			q.add(x);
+		}
+		return q;
+	}
+	
+	private ConcurrentReadInputStream makeCris(FileFormat ff){
+		ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff, null);
+		cris.start(); //Start the stream
+		if(verbose){outstream.println("Started cris");}
+		boolean paired=cris.paired();
+		assert(!paired) : "This should not be paired input.";
+		return cris;
+	}
+	
+	private ConcurrentReadOutputStream makeCros(){
+		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, buff, null, false);
+		ros.start(); //Start the stream
+		return ros;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------       Thread Management      ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Spawn process threads */
+	private void spawnThreads(final ConcurrentReadInputStream cris, boolean altData){
+		
+		//Do anything necessary prior to processing
+		
+		//Fill a list with ProcessThreads
+		if(verbose){System.err.println("Spawning "+threads+" threads.");}
+		ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
+		for(int i=0; i<threads; i++){
+			alpt.add(new ProcessThread(cris, i, altData));
+		}
+		
+		//Start the threads and wait for them to finish
+		boolean success=ThreadWaiter.startAndWait(alpt, this);
+		if(verbose){System.err.println("Threads finished with success="+success+".");}
+		errorState&=!success;
+	}
+	
+	@Override
+	public final void accumulate(ProcessThread pt){
+		readsProcessed+=pt.readsProcessedT;
+		basesProcessed+=pt.basesProcessedT;
+		errorState|=(!pt.success);
+	}
+	
+	@Override
+	public final boolean success(){return !errorState;}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         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_, boolean alt_){
+			cris=cris_;
+			tid=tid_;
+			processInput=(cris!=null);
+			altData=alt_;
+		}
+		
+		//Called by start()
+		@Override
+		public void run(){
+			//Do anything necessary prior to processing
+			
+			if(processInput){
+				//Process the reads
+				processInner();
+			}else{
+				pickBest();
+			}
+			
+			//Do anything necessary after processing
+			
+			//Indicate successful exit status
+			success=true;
+		}
+		
+		/** Iterate through the reads */
+		void processInner(){
+			if(verbose && tid==0){System.err.println("processInner() for tid="+tid);}
+			
+			//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
+				
+				processInput(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 processInput(ListNum<Read> ln){
+			if(verbose && tid==0){System.err.println("processInput() for tid="+tid);}
+
+			//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);
+				
+				//Validate reads in worker threads
+				if(!r1.validated()){r1.validate(true);}
+
+				//Track the initial length for statistics
+				final int initialLength1=r1.length();
+
+				//Increment counters
+				readsProcessedT++;
+				basesProcessedT+=initialLength1;
+				
+				processRead(r1);
+			}
+		}
+		
+		void pickBest(){
+			if(verbose && tid==0){System.err.println("pickBest() for tid="+tid);}
+			for(ArrayList<Ribo> list=queue.poll(); list!=null; list=queue.poll()){
+				Ribo best=pickBest(list);
+				list.clear();
+				synchronized(bestList){
+					bestList.add(best);
+				}
+			}
+		}
+		
+		Ribo pickBest(ArrayList<Ribo> list){
+			if(verbose && tid==0){System.err.println("pickBest(list[="+list.size()+"]) for tid="+tid);}
+			assert(list!=null && list.size()>0);
+			if(list.size()==1){return list.get(0);}
+			Collections.sort(list);
+			Collections.reverse(list);
+			assert(list.get(0).product>=list.get(1).product);
+			if(list.size()<3 || fast){return list.get(0);}
+			
+			Ribo base=list.get(0);
+			int pad=Tools.max(10, (1600-base.r.length()));
+			BaseGraph bg=new BaseGraph(base.r.name(), base.r.bases, base.r.quality, base.r.numericID, pad);
+			for(Ribo r : list){
+				bg.alignAndGenerateMatch(r.r, ssa);
+			}
+			Read consensus=bg.traverse();
+			Ribo best;
+			if(useConsensus){
+				best=new Ribo(consensus, base.tid, 1);
+			}else{
+				for(Ribo r : list){
+					float id=align(r.r.bases, consensus.bases);
+					r.identity=id;
+					r.product=score(r.length(), r.identity);
+				}
+				Collections.sort(list);
+				Collections.reverse(list);
+				assert(list.get(0).product>=list.get(1).product);
+				best=list.get(0);
+			}
+			return best;
+		}
+		
+		/**
+		 * Process a read or a read pair.
+		 * @return True if the reads should be kept, false if they should be discarded.
+		 */
+		void processRead(final Read r){
+			if(verbose && tid==0){System.err.println("processRead()");}
+			if(r.length()<minlen || r.length()>maxlen){return;}
+			if(maxns>=0 && r.countNocalls()>maxns){return;}
+			Integer key=GiToTaxid.parseTaxidNumber(r.id, '|');
+			if(verbose && tid==0){System.err.println("key="+key);}
+			if(key==null || key==-1 || (altData && seenTaxID.contains(key))){return;}
+			float id=align(r);
+			if(id<minID){return;}
+			Ribo ribo=new Ribo(r, key, id);
+			
+			synchronized(listMap){
+				ArrayList<Ribo> list=listMap.get(key);
+				if(list==null){
+					list=new ArrayList<Ribo>(8);
+					listMap.put(key, list);
+				}
+				list.add(ribo);
+				if(!altData){seenTaxID.add(key);}
+			}
+		}
+		
+		float align(Read r){
+			float a=(process16S ? align(r.bases, consensus16S) : 0);
+			float b=(process18S ? align(r.bases, consensus18S) : 0);
+			if(verbose && tid==0){System.err.println("Aligned; a="+a+", b="+b);}
+			return Tools.max(a, b);
+		}
+		
+		float align(byte[] query, byte[] ref){
+			int a=0, b=ref.length-1;
+			int[] max=ssa.fillUnlimited(query, ref, a, b, -9999);
+			if(max==null){return 0;}
+			
+			final int rows=max[0];
+			final int maxCol=max[1];
+			final int maxState=max[2];
+			final float id=ssa.tracebackIdentity(query, ref, a, b, rows, maxCol, maxState, null);
+			return id;
+		}
+		
+		SingleStateAlignerFlat2 ssa=new SingleStateAlignerFlat2();
+
+		/** Number of reads processed by this thread */
+		protected long readsProcessedT=0;
+		/** Number of bases processed by this thread */
+		protected long basesProcessedT=0;
+		
+		/** True only if this thread has completed successfully */
+		boolean success=false;
+		
+		/** Shared input stream */
+		private final ConcurrentReadInputStream cris;
+		/** Thread ID */
+		final int tid;
+		
+		//Run mode
+		final boolean processInput;
+		final boolean altData;
+	}
+	
+	private class Ribo implements Comparable<Ribo>{
+		Ribo(Read r_, int tid_, float identity_){
+			r=r_;
+			tid=tid_;
+			identity=identity_;
+			product=score(r.length(), identity);
+		}
+		
+		@Override
+		public int compareTo(Ribo b) {
+			if(b.product>product){return -1;}
+			else if(b.product<product){return 1;}
+			else if(b.r.length()>r.length()){return -1;}
+			else if(b.r.length()<r.length()){return 1;}
+			return 0;
+		}
+		
+		int length(){return r.length();}
+		
+		Read r;
+		int tid;
+		float identity;
+		float product;
+	}
+	
+	private class ListComparator implements Comparator<ArrayList<Ribo>> {
+
+		@Override
+		public int compare(ArrayList<Ribo> a, ArrayList<Ribo> b) {
+			return a.size()>b.size() ? -1 : a.size()<b.size() ? 1 : 0;
+		}
+		
+	}
+	
+	private float lengthMult(int len){
+		int idealLength=idealLength();
+		int max=Tools.max(len, idealLength, 1);
+		int min=Tools.min(len, idealLength);
+		return min/(float)max;
+	}
+	
+	private float score(int len, float identity){
+		return lengthMult(len)*identity;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Primary input file path */
+	private ArrayList<String> in=new ArrayList<String>();
+	
+	/** Alternate input file path */
+	private String alt=null;
+	
+	/** Primary output file path */
+	private String out1=null;
+	
+	/** Override input file extension */
+	private String extin=null;
+	/** Override output file extension */
+	private String extout=null;
+
+	ArrayList<Ribo> bestList=new ArrayList<Ribo>();
+	HashMap<Integer, ArrayList<Ribo>> listMap=new HashMap<Integer, ArrayList<Ribo>>(100000);
+	ConcurrentLinkedQueue<ArrayList<Ribo>> queue;
+	
+	
+	IntHashSet seenTaxID=new IntHashSet(1000000);
+	
+	byte[] consensus16S;
+	byte[] consensus18S;
+	
+	int idealLength(){
+		if(process16S){return consensus16S.length;}
+		return consensus18S.length;
+	}
+	
+	boolean useConsensus=false;
+	boolean fast=false;
+	int maxns=-1;
+	int minlen=1;
+	int maxlen=4000;
+	
+	/*--------------------------------------------------------------*/
+
+	/** 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;
+
+	private float minID=0.62f;
+	
+	private boolean process16S=true;
+	private boolean process18S=false;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary input file */
+	private final ArrayList<FileFormat> ffin;
+	private final FileFormat ffalt;
+	
+	/** Primary output file */
+	private final FileFormat ffout1;
+	
+	final int threads;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        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;
+	
+}