jpayne@68: package clump;
jpayne@68: 
jpayne@68: import java.io.File;
jpayne@68: import java.io.PrintStream;
jpayne@68: import java.util.ArrayList;
jpayne@68: 
jpayne@68: import bloom.KCountArray;
jpayne@68: import fileIO.ByteFile;
jpayne@68: import fileIO.FileFormat;
jpayne@68: import fileIO.ReadWrite;
jpayne@68: import jgi.BBMerge;
jpayne@68: import shared.KillSwitch;
jpayne@68: import shared.Parse;
jpayne@68: import shared.Parser;
jpayne@68: import shared.PreParser;
jpayne@68: import shared.ReadStats;
jpayne@68: import shared.Shared;
jpayne@68: import shared.Timer;
jpayne@68: import shared.Tools;
jpayne@68: import stream.ConcurrentReadInputStream;
jpayne@68: import stream.ConcurrentReadOutputStream;
jpayne@68: import stream.FASTQ;
jpayne@68: import stream.FastaReadInputStream;
jpayne@68: import stream.Read;
jpayne@68: import structures.ListNum;
jpayne@68: import structures.Quantizer;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date June 20, 2014
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class KmerSplit {
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Initialization        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * Code entrance from the command line.
jpayne@68: 	 * @param args Command line arguments
jpayne@68: 	 */
jpayne@68: 	public static void main(String[] args){
jpayne@68: 		final boolean pigz=ReadWrite.USE_PIGZ, unpigz=ReadWrite.USE_UNPIGZ;
jpayne@68: 		final boolean oldFInt=FASTQ.FORCE_INTERLEAVED, oldTInt=FASTQ.TEST_INTERLEAVED;
jpayne@68: 		final int zl=ReadWrite.ZIPLEVEL;
jpayne@68: 		final float ztd=ReadWrite.ZIP_THREAD_MULT;
jpayne@68: 		final int mzt=ReadWrite.MAX_ZIP_THREADS;
jpayne@68: 		Timer t=new Timer();
jpayne@68: 		KmerSplit x=new KmerSplit(args);
jpayne@68: 		ReadWrite.ZIPLEVEL=Tools.min(ReadWrite.ZIPLEVEL, maxZipLevel);
jpayne@68: 		x.process(t);
jpayne@68: 		ReadWrite.USE_PIGZ=pigz;
jpayne@68: 		ReadWrite.USE_UNPIGZ=unpigz;
jpayne@68: 		ReadWrite.ZIPLEVEL=zl;
jpayne@68: 		ReadWrite.ZIP_THREAD_MULT=ztd;
jpayne@68: 		ReadWrite.MAX_ZIP_THREADS=mzt;
jpayne@68: 		FASTQ.FORCE_INTERLEAVED=oldFInt;
jpayne@68: 		FASTQ.TEST_INTERLEAVED=oldTInt;
jpayne@68: 		
jpayne@68: 		//Close the print stream if it was redirected
jpayne@68: 		Shared.closeStream(x.outstream);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * Constructor.
jpayne@68: 	 * @param args Command line arguments
jpayne@68: 	 */
jpayne@68: 	public KmerSplit(String[] args){
jpayne@68: 		
jpayne@68: 		{//Preparse block for help, config files, and outstream
jpayne@68: 			PreParser pp=new PreParser(args, getClass(), false);
jpayne@68: 			args=pp.args;
jpayne@68: 			outstream=pp.outstream;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		ReadWrite.USE_PIGZ=false;
jpayne@68: 		ReadWrite.USE_UNPIGZ=true;
jpayne@68: 		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
jpayne@68: 
jpayne@68: 		boolean setInterleaved=false; //Whether it was explicitly set.
jpayne@68: 		Parser parser=new Parser();
jpayne@68: 		
jpayne@68: 		for(int i=0; i<args.length; i++){
jpayne@68: 			String arg=args[i];
jpayne@68: 			String[] split=arg.split("=");
jpayne@68: 			String a=split[0].toLowerCase();
jpayne@68: 			String b=split.length>1 ? split[1] : null;
jpayne@68: 
jpayne@68: 			if(parser.parse(arg, a, b)){
jpayne@68: 				//do nothing
jpayne@68: 			}else if(a.equals("verbose")){
jpayne@68: 				verbose=KmerComparator.verbose=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("parse_flag_goes_here")){
jpayne@68: 				//Set a variable here
jpayne@68: 			}else if(a.equals("k")){
jpayne@68: 				k=Integer.parseInt(b);
jpayne@68: 				assert(k>0 && k<32);
jpayne@68: 			}else if(a.equals("mincount") || a.equals("mincr")){
jpayne@68: 				minCount=Integer.parseInt(b);
jpayne@68: 			}else if(a.equals("groups") || a.equals("g") || a.equals("sets") || a.equals("ways")){
jpayne@68: 				groups=Integer.parseInt(b);
jpayne@68: 			}else if(a.equals("rename") || a.equals("addname")){
jpayne@68: 				//Do nothing
jpayne@68: //				addName=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("shortname") || a.equals("shortnames")){
jpayne@68: 				if(b!=null && b.equals("shrink")){
jpayne@68: 					shrinkName=true;
jpayne@68: 				}else{
jpayne@68: 					shrinkName=false;
jpayne@68: 					shortName=Parse.parseBoolean(b);
jpayne@68: 				}
jpayne@68: 			}else if(a.equals("rcomp") || a.equals("reversecomplement")){
jpayne@68: 				//ignore rcomp=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("condense") || a.equals("consensus") || a.equals("concensus")){//Note the last one is intentionally misspelled
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("correct") || a.equals("ecc")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("passes")){
jpayne@68: 				int x=Integer.parseInt(b);
jpayne@68: //				if(x>1){outstream.println("Warning: KmerSplit does not support multiple passes.");}
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			else if(a.equals("dedupe")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("entryfilter")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("markduplicates")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("markall")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("addcount") || a.equals("renamebycount")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("optical") || a.equals("opticalonly")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("dupesubs") || a.equals("duplicatesubs") || a.equals("dsubs") || a.equals("subs") || a.equals("s")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("dupedist") || a.equals("duplicatedistance") || a.equals("ddist") || a.equals("dist") || a.equals("opticaldist") || a.equals("distance")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("scanlimit") || a.equals("scan")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("removeallduplicates") || a.equals("allduplicates")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("allowns")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("containment") || a.equals("absorbcontainment") || a.equals("ac") || a.equals("contains")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equalsIgnoreCase("prefixOrSuffix") || a.equalsIgnoreCase("suffixOrPrefix") || a.equals("affix") || a.equals("pos")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("printduplicates")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("dupeidentity")){
jpayne@68: 				//ignore
jpayne@68: 			}else if(a.equals("dupesubrate") || a.equals("dsr") || a.equals("subrate")){
jpayne@68: 				//ignore
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			else if(a.equals("prefilter")){
jpayne@68: 				KmerReduce.prefilter=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("ecco")){
jpayne@68: 				ecco=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("seed")){
jpayne@68: 				KmerComparator.defaultSeed=Long.parseLong(b);
jpayne@68: 			}else if(a.equals("hashes")){
jpayne@68: 				KmerComparator.setHashes(Integer.parseInt(b));
jpayne@68: 			}else if(a.equals("border")){
jpayne@68: 				KmerComparator.defaultBorder=Integer.parseInt(b);
jpayne@68: 			}else if(a.equals("minprob")){
jpayne@68: 				KmerComparator.minProb=Float.parseFloat(b);
jpayne@68: 			}else if(a.equals("unpair")){
jpayne@68: 				unpair=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("repair")){
jpayne@68: 				//Do nothing
jpayne@68: 			}else if(a.equals("namesort") || a.equals("sort")){
jpayne@68: 				//Do nothing
jpayne@68: 			}else if(a.equals("fetchthreads")){
jpayne@68: 				//Do nothing
jpayne@68: 			}else if(a.equals("reorder") || a.equals("reorderclumps")){
jpayne@68: 				//reorder=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("reorderpaired") || a.equals("reorderclumpspaired")){
jpayne@68: //				reorderpaired=Parse.parseBoolean(b);
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			
jpayne@68: 			else if(Clump.parseStatic(arg, a, b)){
jpayne@68: 				//Do nothing
jpayne@68: 			}
jpayne@68: 				
jpayne@68: 			else{
jpayne@68: 				outstream.println("Unknown parameter "+args[i]);
jpayne@68: 				assert(false) : "Unknown parameter "+args[i];
jpayne@68: 				//				throw new RuntimeException("Unknown parameter "+args[i]);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		{//Process parser fields
jpayne@68: 			Parser.processQuality();
jpayne@68: 			
jpayne@68: 			maxReads=parser.maxReads;
jpayne@68: 			
jpayne@68: 			overwrite=ReadStats.overwrite=parser.overwrite;
jpayne@68: 			append=ReadStats.append=parser.append;
jpayne@68: 
jpayne@68: 			setInterleaved=parser.setInterleaved;
jpayne@68: 			
jpayne@68: 			in1=parser.in1;
jpayne@68: 			in2=parser.in2;
jpayne@68: 
jpayne@68: 			out1=parser.out1;
jpayne@68: 			
jpayne@68: 			extin=parser.extin;
jpayne@68: 			extout=parser.extout;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(groups>2){ReadWrite.USE_PIGZ=false;}
jpayne@68: 		
jpayne@68: 		if(in1!=null && in2==null && in1.indexOf('#')>-1 && !new File(in1).exists()){
jpayne@68: 			in2=in1.replace("#", "2");
jpayne@68: 			in1=in1.replace("#", "1");
jpayne@68: 		}
jpayne@68: 		if(in2!=null){
jpayne@68: 			if(FASTQ.FORCE_INTERLEAVED){outstream.println("Reset INTERLEAVED to false because paired input files were specified.");}
jpayne@68: 			FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		assert(FastaReadInputStream.settingsOK());
jpayne@68: 		
jpayne@68: 		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
jpayne@68: 		if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
jpayne@68: 			ByteFile.FORCE_MODE_BF2=true;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(!setInterleaved){
jpayne@68: 			assert(in1!=null) : "\nin1="+in1+"\nin2="+in2+"\nout1="+out1+"\n";
jpayne@68: 			if(in2!=null){ //If there are 2 input streams.
jpayne@68: 				FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
jpayne@68: 				outstream.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		if(out1!=null && out1.equalsIgnoreCase("null")){out1=null;}
jpayne@68: 		
jpayne@68: 		if(out1!=null){
jpayne@68: 			assert(out1.contains("%"));
jpayne@68: 			outArray=new String[groups];
jpayne@68: 			for(int i=0; i<groups; i++){
jpayne@68: 				outArray[i]=out1.replaceFirst("%", ""+i);
jpayne@68: 			}
jpayne@68: 			if(!Tools.testOutputFiles(overwrite, append, false, outArray)){
jpayne@68: 				outstream.println((out1==null)+", "+out1);
jpayne@68: 				throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+"\n");
jpayne@68: 			}
jpayne@68: 			ffout=new FileFormat[groups];
jpayne@68: 			if(groups>1){ReadWrite.setZipThreadMult(Tools.min(0.5f, 2f/(groups+1)));}
jpayne@68: 			for(int i=0; i<groups; i++){
jpayne@68: 				ffout[i]=FileFormat.testOutput(outArray[i], FileFormat.FASTQ, extout, groups<10, overwrite, append, false);
jpayne@68: 			}
jpayne@68: 		}else{
jpayne@68: 			outArray=null;
jpayne@68: 			throw new RuntimeException("out is a required parameter.");
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
jpayne@68: 		ffin2=FileFormat.testInput(in2, FileFormat.FASTQ, extin, true, true);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Outer Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/** Count kmers */
jpayne@68: 	void preprocess(){
jpayne@68: 		if(minCount>1){
jpayne@68: 			table=ClumpTools.getTable(in1, in2, k, minCount);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	/** Create read streams and process all data */
jpayne@68: 	void process(Timer t){
jpayne@68: 		
jpayne@68: 		preprocess();
jpayne@68: 		
jpayne@68: 		final ConcurrentReadInputStream cris;
jpayne@68: 		{
jpayne@68: 			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, null, null);
jpayne@68: 			cris.start();
jpayne@68: 			if(verbose){outstream.println("Started cris");}
jpayne@68: 		}
jpayne@68: 		boolean paired=cris.paired();
jpayne@68: 		if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
jpayne@68: 		if(cris.paired() && (in1==null || !in1.contains(".sam") && !unpair)){
jpayne@68: 			outstream.println("Writing interleaved.");
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		final ConcurrentReadOutputStream ros[]=new ConcurrentReadOutputStream[groups];
jpayne@68: 		try {
jpayne@68: 			for(int i=0; i<groups; i++){
jpayne@68: 				final int buff=8;
jpayne@68: 
jpayne@68: 				assert(!out1.equalsIgnoreCase(in1) && !out1.equalsIgnoreCase(in1)) : "Input file and output file have same name.";
jpayne@68: 				
jpayne@68: 				ros[i]=ConcurrentReadOutputStream.getStream(ffout[i], null, null, null, buff, null, false);
jpayne@68: 				ros[i].start();
jpayne@68: 			}
jpayne@68: 		} catch (OutOfMemoryError e) {
jpayne@68: 			KillSwitch.memKill(e);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		readsProcessed=0;
jpayne@68: 		basesProcessed=0;
jpayne@68: 		
jpayne@68: 		//Process the read stream
jpayne@68: 		processInner(cris, ros);
jpayne@68: 		
jpayne@68: 		errorState|=ReadStats.writeAll();
jpayne@68: 		
jpayne@68: 		t.stop();
jpayne@68: 		
jpayne@68: 		outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
jpayne@68: 		
jpayne@68: 		if(errorState){
jpayne@68: 			Clumpify.sharedErrorState=true;
jpayne@68: 			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Collect and sort the reads */
jpayne@68: 	void processInner(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream[] ros){
jpayne@68: 		if(verbose){outstream.println("Making comparator.");}
jpayne@68: 		KmerComparator kc=new KmerComparator(k, false, false);
jpayne@68: 		if(verbose){outstream.println("Seed: "+kc.seed);}
jpayne@68: 		
jpayne@68: 		if(verbose){outstream.println("Splitting reads.");}
jpayne@68: 		splitReads(cris, ros, kc);
jpayne@68: 		lastMemProcessed=memProcessed;
jpayne@68: 		
jpayne@68: 		if(verbose){outstream.println("Done!");}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void splitReads(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream[] ros, final KmerComparator kc){
jpayne@68: 		Timer t=new Timer();
jpayne@68: 		if(verbose){t.start("Making hash threads.");}
jpayne@68: 		final int threads=Shared.threads();
jpayne@68: 		ArrayList<HashThread> alht=new ArrayList<HashThread>(threads);
jpayne@68: 		for(int i=0; i<threads; i++){alht.add(new HashThread(i, cris, ros, kc));}
jpayne@68: 		
jpayne@68: 		if(verbose){outstream.println("Starting threads.");}
jpayne@68: 		for(HashThread ht : alht){ht.start();}
jpayne@68: 		
jpayne@68: 		
jpayne@68: 		if(verbose){outstream.println("Waiting for threads.");}
jpayne@68: 		/* Wait for threads to die */
jpayne@68: 		for(HashThread ht : alht){
jpayne@68: 			
jpayne@68: 			/* Wait for a thread to die */
jpayne@68: 			while(ht.getState()!=Thread.State.TERMINATED){
jpayne@68: 				try {
jpayne@68: 					ht.join();
jpayne@68: 				} catch (InterruptedException e) {
jpayne@68: 					e.printStackTrace();
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			readsProcessed+=ht.readsProcessedT;
jpayne@68: 			basesProcessed+=ht.basesProcessedT;
jpayne@68: 			diskProcessed+=ht.diskProcessedT;
jpayne@68: 			memProcessed+=ht.memProcessedT;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(verbose){outstream.println("Closing streams.");}
jpayne@68: 		errorState=ReadWrite.closeStreams(cris, ros)|errorState;
jpayne@68: 		if(verbose){t.stop("Split time: ");}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Inner Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Inner Classes        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	private class HashThread extends Thread{
jpayne@68: 
jpayne@68: 		HashThread(int id_, ConcurrentReadInputStream cris_, ConcurrentReadOutputStream[] ros_, KmerComparator kc_){
jpayne@68: 			id=id_;
jpayne@68: 			cris=cris_;
jpayne@68: 			ros=ros_;
jpayne@68: 			kc=kc_;
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		@Override
jpayne@68: 		public void run(){
jpayne@68: 
jpayne@68: 			final boolean paired=cris.paired();
jpayne@68: 			ListNum<Read> ln=cris.nextList();
jpayne@68: 			ArrayList<Read> reads=(ln!=null ? ln.list : null);
jpayne@68: 			
jpayne@68: 			ArrayList<Read>[] array=new ArrayList[groups];
jpayne@68: 			for(int i=0; i<groups; i++){
jpayne@68: 				array[i]=new ArrayList<Read>(buffer);
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
jpayne@68: 				
jpayne@68: 				for(Read r : reads){
jpayne@68: 					if(!r.validated()){
jpayne@68: 						r.validate(true);
jpayne@68: 						if(r.mate!=null){r.mate.validate(true);}
jpayne@68: 					}
jpayne@68: 					readsProcessedT+=1+r.mateCount();
jpayne@68: 					basesProcessedT+=r.length()+r.mateLength();
jpayne@68: 					diskProcessedT+=r.countFastqBytes()+r.countMateFastqBytes();
jpayne@68: 					memProcessedT+=r.countBytes()+r.countMateBytes()+ReadKey.overhead;
jpayne@68: 					if(shrinkName){
jpayne@68: 						Clumpify.shrinkName(r);
jpayne@68: 						Clumpify.shrinkName(r.mate);
jpayne@68: 					}else if(shortName){
jpayne@68: 						Clumpify.shortName(r);
jpayne@68: 						Clumpify.shortName(r.mate);
jpayne@68: 					}
jpayne@68: 					
jpayne@68: 					if(quantizeQuality){
jpayne@68: 						Quantizer.quantize(r, r.mate);
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 				
jpayne@68: 				if(ecco){
jpayne@68: 					for(Read r : reads){
jpayne@68: 						if(r.mate!=null){BBMerge.findOverlapStrict(r, r.mate, true);}
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 				
jpayne@68: 				ArrayList<Read> hashList=reads;
jpayne@68: 				if(paired && unpair){
jpayne@68: 					hashList=new ArrayList<Read>(reads.size()*2);
jpayne@68: 					for(Read r1 : reads){
jpayne@68: 						Read r2=r1.mate;
jpayne@68: 						hashList.add(r1);
jpayne@68: 						hashList.add(r2);
jpayne@68: 						r1.mate=null;
jpayne@68: 						r2.mate=null;
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 				
jpayne@68: 				kc.hash(hashList, table, minCount, true);
jpayne@68: 				for(Read r : hashList){
jpayne@68: 					long kmer=((ReadKey)r.obj).kmer;
jpayne@68: 					long code=kc.hash(kmer);
jpayne@68: 					int code2=(int)(code%groups);
jpayne@68: 					assert(code2>=0 && code2<array.length) : code2+", "+groups+", "+array.length+", "+kmer+", "+r.obj+"\n"+r;
jpayne@68: 					array[code2].add(r);
jpayne@68: 					if(array[code2].size()>=buffer){
jpayne@68: 						ros[code2].add(array[code2], 0);
jpayne@68: 						array[code2]=new ArrayList<Read>(buffer);
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 				cris.returnList(ln);
jpayne@68: 				ln=cris.nextList();
jpayne@68: 				reads=(ln!=null ? ln.list : null);
jpayne@68: 			}
jpayne@68: 			if(ln!=null){
jpayne@68: 				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
jpayne@68: 			}
jpayne@68: 			for(int i=0; i<groups; i++){
jpayne@68: 				if(!array[i].isEmpty()){
jpayne@68: 					ros[i].add(array[i], 0);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		final int id;
jpayne@68: 		final ConcurrentReadInputStream cris;
jpayne@68: 		final ConcurrentReadOutputStream[] ros;
jpayne@68: 		final KmerComparator kc;
jpayne@68: 		static final int buffer=200;
jpayne@68: 		
jpayne@68: 		protected long readsProcessedT=0;
jpayne@68: 		protected long basesProcessedT=0;
jpayne@68: 		protected long diskProcessedT=0;
jpayne@68: 		protected long memProcessedT=0;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	private int k=31;
jpayne@68: 	int groups=16;
jpayne@68: 	int minCount=0;
jpayne@68: 	
jpayne@68: 	KCountArray table=null;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------          I/O Fields          ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	private String in1=null;
jpayne@68: 	private String in2=null;
jpayne@68: 
jpayne@68: 	private String out1=null;
jpayne@68: 	private String[] outArray=null;
jpayne@68: 	
jpayne@68: 	private String extin=null;
jpayne@68: 	private String extout=null;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	protected long readsProcessed=0;
jpayne@68: 	protected long basesProcessed=0;
jpayne@68: 	protected long diskProcessed=0;
jpayne@68: 	protected long memProcessed=0;
jpayne@68: 	
jpayne@68: 	protected static long lastMemProcessed=0;
jpayne@68: 	
jpayne@68: 	private long maxReads=-1;
jpayne@68: //	private boolean addName=false;
jpayne@68: 	boolean shortName=false;
jpayne@68: 	boolean shrinkName=false;
jpayne@68: 	boolean ecco=false;
jpayne@68: 	boolean unpair=false;
jpayne@68: 	
jpayne@68: 	static int maxZipLevel=2;
jpayne@68: 
jpayne@68: 	static boolean quantizeQuality=false;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Final Fields         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	private final FileFormat ffin1;
jpayne@68: 	private final FileFormat ffin2;
jpayne@68: 	
jpayne@68: 	private final FileFormat[] ffout;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Common Fields         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	private PrintStream outstream=System.err;
jpayne@68: 	public static boolean verbose=false;
jpayne@68: 	public boolean errorState=false;
jpayne@68: 	private boolean overwrite=false;
jpayne@68: 	private boolean append=false;
jpayne@68: 	
jpayne@68: }