csp2: CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/SketchTool.java comparison

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/SketchTool.java @ 68:5028fdace37b

planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d

author	jpayne
date	Tue, 18 Mar 2025 16:23:26 -0400
parents
children

comparison

equal deleted inserted replaced

-:0e9998148a16
+:5028fdace37b
+package sketch;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.concurrent.ConcurrentLinkedQueue;
+import java.util.concurrent.atomic.AtomicInteger;
+import dna.AminoAcid;
+import fileIO.ByteFile;
+import fileIO.ByteStreamWriter;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import kmer.HashArray1D;
+import kmer.HashForest;
+import kmer.KmerNode;
+import kmer.KmerTableSet;
+import shared.KillSwitch;
+import shared.Parse;
+import shared.Shared;
+import shared.Tools;
+import stream.ConcurrentReadInputStream;
+import stream.Read;
+import structures.ByteBuilder;
+import structures.IntList;
+import structures.ListNum;
+import structures.LongList;
+import structures.StringNum;
+/**
+* @author Brian Bushnell
+* @date June 28, 2016
+*
+*/
+public final class SketchTool extends SketchObject {
+	/*--------------------------------------------------------------*/
+	/*----------------         Constructor          ----------------*/
+	/*--------------------------------------------------------------*/
+	public SketchTool(int size_, DisplayParams params){
+		this(size_, params.minKeyOccuranceCount, params.trackCounts(), params.mergePairs);
+	}
+	public SketchTool(int size_, int minKeyOccuranceCount_, boolean trackCounts_, boolean mergePairs_){
+		stTargetSketchSize=size_;
+		minKeyOccuranceCount=minKeyOccuranceCount_;
+		trackCounts=trackCounts_;
+		mergePairs=mergePairs_;
+		assert(!aminoOrTranslate() || !rcomp) : "rcomp should be false in amino mode.";
+		assert(!aminoOrTranslate() || (k*AminoAcid.AMINO_SHIFT<64)) : "Protein sketches require 1 <= K <= "+(63/AminoAcid.AMINO_SHIFT)+".";
+		assert(k>0 && k<=32) : "Sketches require 1 <= K <= 32."; //123
+	}
+	/*--------------------------------------------------------------*/
+	/*----------------           Methods            ----------------*/
+	/*--------------------------------------------------------------*/
+	public Sketch toSketch(KmerTableSet tables, boolean multithreaded){
+		final int threads=(multithreaded ? Tools.mid(1, Shared.threads(), tables.ways()) : 1);
+		return (threads<2 ? toSketch_ST(tables) : toSketch_MT(tables, threads));
+	}
+	private Sketch toSketch_ST(KmerTableSet tables){
+		SketchHeap heap=(stTargetSketchSize>0 ? new SketchHeap(stTargetSketchSize, minKeyOccuranceCount, trackCounts) : null);
+		LongList list=new LongList();
+		KmerTableSet kts=(KmerTableSet)tables;
+		for(int tnum=0; tnum<kts.ways; tnum++){
+			HashArray1D table=kts.getTable(tnum);
+			if(stTargetSketchSize>0){
+				toHeap(table, heap);
+			}else{
+				toList(table, list);
+			}
+		}
+		return stTargetSketchSize>0 ? new Sketch(heap, false, trackCounts, null) : toSketch(list);//TODO:  Could add counts here
+	}
+	private Sketch toSketch_MT(KmerTableSet tables, final int threads){
+		ArrayList<SketchThread> alst=new ArrayList<SketchThread>(threads);
+		AtomicInteger ai=new AtomicInteger(0);
+		for(int i=0; i<threads; i++){
+			alst.add(new SketchThread(ai, tables));
+		}
+		//Start the threads
+		for(SketchThread pt : alst){
+			pt.start();
+		}
+		ArrayList<SketchHeap> heaps=new ArrayList<SketchHeap>(threads);
+		LongList list=new LongList();
+		for(SketchThread pt : alst){
+			//Wait until this thread has terminated
+			while(pt.getState()!=Thread.State.TERMINATED){
+				try {
+					//Attempt a join operation
+					pt.join();
+				} catch (InterruptedException e) {
+					//Potentially handle this, if it is expected to occur
+					e.printStackTrace();
+				}
+			}
+			if(stTargetSketchSize>=0){
+				if(pt.heap!=null && pt.heap.size()>0){
+					heaps.add(pt.heap);
+				}
+			}else{
+				if(pt.list!=null){list.append(pt.list);}
+				pt.list=null;
+			}
+		}
+		alst.clear();
+		return stTargetSketchSize>=0 ? toSketch(heaps, true) : toSketch(list);//TODO:  Could add counts here
+	}
+	public SketchHeap toHeap(HashArray1D table, SketchHeap heap){
+//		if(heap==null){heap=new LongHeap(size, true);}
+		long[] kmers=table.array();
+		int[] counts=table.values();
+		for(int i=0; i<table.arrayLength(); i++){
+			int count=counts[i];
+			if(count>=minKeyOccuranceCount){
+				heap.genomeSizeKmers++;
+				long kmer=kmers[i];
+				long hashcode=hash(kmer);
+				if(hashcode>=minHashValue){
+					heap.add(hashcode);
+				}
+			}
+		}
+		HashForest forest=table.victims();
+		if(forest!=null){
+			for(KmerNode kn : forest.array()){
+				if(kn!=null){addRecursive(heap, kn);}
+			}
+		}
+		return heap;
+	}
+	public LongList toList(HashArray1D table, LongList list){
+//		if(heap==null){heap=new LongHeap(size, true);}
+		long[] kmers=table.array();
+		int[] counts=table.values();
+		for(int i=0; i<table.arrayLength(); i++){
+			int count=counts[i];
+			if(count>=minKeyOccuranceCount){
+				long kmer=kmers[i];
+				long hashcode=hash(kmer);
+				if(hashcode>=minHashValue){
+					list.add(hashcode);
+				}
+			}
+		}
+		HashForest forest=table.victims();
+		if(forest!=null){
+			for(KmerNode kn : forest.array()){
+				if(kn!=null){addRecursive(list, kn);}
+			}
+		}
+		return list;
+	}
+//	public long[] toSketchArray(ArrayList<LongHeap> heaps){
+//		if(heaps.size()==1){return toSketchArray(heaps.get(0));}
+//		LongList list=new LongList(size);
+//		for(LongHeap heap : heaps){
+//			while(heap.size()>0){list.add(Long.MAX_VALUE-heap.poll());}
+//		}
+//		list.sort();
+//		list.shrinkToUnique();
+//		list.size=Tools.min(size, list.size);
+//		return list.toArray();
+//	}
+	public Sketch toSketch(ArrayList<SketchHeap> heaps, boolean allowZeroSizeSketch){
+		if(heaps==null || heaps.isEmpty()){
+			if(allowZeroSizeSketch){
+				return new Sketch(new long[0], null, null, null, null, null);
+			}else{
+				return null;
+			}
+		}
+		SketchHeap a=heaps.get(0);
+		for(int i=1; i<heaps.size(); i++){
+			SketchHeap b=heaps.get(i);
+			a.add(b);
+		}
+		if(verbose2){System.err.println("Creating a sketch of size "+a.size()+".");}
+		return new Sketch(a, false, trackCounts, null);
+	}
+	Sketch toSketch(LongList list){
+		list.sort();
+		assert(list.size==0 || list.get(list.size()-1)>=minHashValue) : list.size+", "+list.get(list.size()-1)+", "+minHashValue;
+		list.shrinkToUnique();
+		list.reverse();
+		for(int i=0; i<list.size; i++){list.array[i]=Long.MAX_VALUE-list.array[i];}
+		return new Sketch(list.toArray(), null, null, null, null, null);
+	}
+	/*--------------------------------------------------------------*/
+	/*----------------           Helpers            ----------------*/
+	/*--------------------------------------------------------------*/
+	private void addRecursive(SketchHeap heap, KmerNode kn){
+		if(kn==null){return;}
+		if(kn.count()>=minKeyOccuranceCount){
+			heap.genomeSizeKmers++;
+			long kmer=kn.pivot();
+			long hashcode=hash(kmer);
+			if(hashcode>=minHashValue){heap.add(hashcode);}
+		}
+		if(kn.left()!=null){addRecursive(heap, kn.left());}
+		if(kn.right()!=null){addRecursive(heap, kn.right());}
+	}
+	private void addRecursive(LongList list, KmerNode kn){
+		if(kn==null){return;}
+		if(kn.count()>=minKeyOccuranceCount){
+			long kmer=kn.pivot();
+			long hashcode=hash(kmer);
+			if(hashcode>=minHashValue){list.add(hashcode);}
+		}
+		if(kn.left()!=null){addRecursive(list, kn.left());}
+		if(kn.right()!=null){addRecursive(list, kn.right());}
+	}
+	/*--------------------------------------------------------------*/
+	/*----------------             I/O              ----------------*/
+	/*--------------------------------------------------------------*/
+//	public static ArrayList<Sketch> loadSketches_ST(String...fnames){
+//		ArrayList<Sketch> sketches=null;
+//		for(String s : fnames){
+//			ArrayList<Sketch> temp;
+//			if(s.indexOf(',')<0 || s.startsWith("stdin") || new File(s).exists()){
+//				temp=loadSketches(s);
+//			}else{
+//				temp=loadSketches_ST(s.split(","));
+//			}
+//			if(sketches==null){sketches=temp;}
+//			else{sketches.addAll(temp);}
+//		}
+//		return sketches;
+//	}
+//	public static ArrayList<Sketch> loadSketches_MT(ArrayList<String> fnames){
+//		return loadSketches_MT(0, null, fnames.toArray(new String[0]));
+//	}
+	public ArrayList<Sketch> loadSketches_MT(DisplayParams params, Collection<String> fnames){
+		return loadSketches_MT(params.mode, params.samplerate, params.maxReads,
+				params.minEntropy, params.minProb, params.minQual, fnames);
+	}
+	public ArrayList<Sketch> loadSketches_MT(DisplayParams params, String...fnames){
+		return loadSketches_MT(params.mode, params.samplerate, params.maxReads,
+				params.minEntropy, params.minProb, params.minQual, fnames);
+	}
+	public ArrayList<Sketch> loadSketches_MT(int mode, float samplerate, long reads, float minEntropy, float minProb, byte minQual, Collection<String> fnames){
+		return loadSketches_MT(mode, samplerate, reads, minEntropy, minProb, minQual, fnames.toArray(new String[0]));
+	}
+	//TODO: This is only multithreaded per file in persequence mode.
+	public ArrayList<Sketch> loadSketches_MT(int mode, float samplerate, long reads, float minEntropy, float minProb, byte minQual, String...fnames){
+		ConcurrentLinkedQueue<StringNum> decomposedFnames=new ConcurrentLinkedQueue<StringNum>();
+		int num=0;
+		for(String s : fnames){
+			if(s.indexOf(',')<0 || s.startsWith("stdin") || new File(s).exists()){
+				num++;
+				decomposedFnames.add(new StringNum(s, num));
+			}else{
+				for(String s2 : s.split(",")){
+					num++;
+					decomposedFnames.add(new StringNum(s2, num));
+				}
+			}
+		}
+		if(decomposedFnames.size()==0){return null;}
+		if(decomposedFnames.size()==1){return loadSketchesFromFile(decomposedFnames.poll().s, null, 0, reads, mode, samplerate, minEntropy, minProb, minQual, false);}
+		//Determine how many threads may be used
+		final int threads=Tools.min(Shared.threads(), decomposedFnames.size());
+		//Fill a list with LoadThreads
+		ArrayList<LoadThread> allt=new ArrayList<LoadThread>(threads);
+		for(int i=0; i<threads; i++){
+			allt.add(new LoadThread(decomposedFnames, mode, samplerate, reads, minEntropy, minProb, minQual));
+		}
+		ArrayList<Sketch> sketches=new ArrayList<Sketch>();
+		//Start the threads
+		for(LoadThread lt : allt){lt.start();}
+		//Wait for completion of all threads
+		boolean success=true;
+		for(LoadThread lt : allt){
+			//Wait until this thread has terminated
+			while(lt.getState()!=Thread.State.TERMINATED){
+				try {
+					//Attempt a join operation
+					lt.join();
+				} catch (InterruptedException e) {
+					//Potentially handle this, if it is expected to occur
+					e.printStackTrace();
+				}
+			}
+			sketches.addAll(lt.list);
+			success&=lt.success;
+		}
+		assert(success) : "Failure loading some files.";
+		return sketches;
+	}
+	/*--------------------------------------------------------------*/
+	public ArrayList<Sketch> loadSketchesFromFile(final String fname0, SketchMakerMini smm,
+			int maxThreads, long reads, int mode, DisplayParams params, boolean allowZeroSizeSketch){
+		return loadSketchesFromFile(fname0, smm, maxThreads, reads, mode,
+				params.samplerate, params.minEntropy, params.minProb, params.minQual, allowZeroSizeSketch);
+	}
+	public ArrayList<Sketch> loadSketchesFromFile(final String fname0, SketchMakerMini smm,
+			int maxThreads, long reads, int mode, float samplerate, float minEntropy, float minProb, byte minQual, boolean allowZeroSizeSketch){
+		assert(fname0!=null);//123
+		if(fname0==null){return null;}
+		FileFormat ff=FileFormat.testInput(fname0, FileFormat.FASTA, null, false, true);
+		if(ff.isSequence()){
+			return loadSketchesFromSequenceFile(ff, smm, maxThreads, reads, mode, samplerate, minEntropy, minProb, minQual, allowZeroSizeSketch);
+		}else{
+			return SketchObject.LOADER2 ? loadSketchesFromSketchFile2(ff, allowZeroSizeSketch) : loadSketchesFromSketchFile(ff, allowZeroSizeSketch);
+		}
+	}
+	private ArrayList<Sketch> loadSketchesFromSequenceFile(final FileFormat ff, SketchMakerMini smm,
+			int maxThreads, long reads, int mode, float samplerate, float minEntropy, float minProb, byte minQual, boolean allowZeroSizeSketch){
+		maxThreads=(maxThreads<1 ? Shared.threads() : Tools.min(maxThreads, Shared.threads()));
+//		assert(false) : (ff.fasta() || ff.fastq() || ff.samOrBam())+", "+ff.fastq()+", "+maxThreads+", "+
+//				allowMultithreadedFastq+", "+forceDisableMultithreadedFastq+", "+(mode==ONE_SKETCH);
+		if(ff.fastq() && allowMultithreadedFastq && !forceDisableMultithreadedFastq && (mode==ONE_SKETCH || mode==PER_FILE) &&
+				maxThreads>1 && Shared.threads()>2 && (reads<1 || reads*samplerate*(mergePairs ? 2 : 1)>=1000)){//limit is low due to PacBio long reads
+			final boolean vic=Read.VALIDATE_IN_CONSTRUCTOR;
+			Read.VALIDATE_IN_CONSTRUCTOR=false;
+			if(verbose2){System.err.println("Loading a sketch multithreaded.");}
+			Sketch sketch=processReadsMT(ff.name(), maxThreads, reads, mode, samplerate, minEntropy, minProb, minQual, allowZeroSizeSketch);
+			Read.VALIDATE_IN_CONSTRUCTOR=vic;
+			ArrayList<Sketch> list=new ArrayList<Sketch>(1);
+			if(sketch!=null && (sketch.length()>0 || allowZeroSizeSketch)){
+				sketch.loadSSU();
+				list.add(sketch);
+			}
+			return list;
+		}
+		if(smm==null){smm=new SketchMakerMini(this, mode, minEntropy, minProb, minQual);}
+		if(verbose2){System.err.println("Loading sketches via SMM.");}
+		ArrayList<Sketch> sketches=smm.toSketches(ff.name(), samplerate, reads);
+		if(verbose2){System.err.println("Loaded "+(sketches==null ? 0 : sketches.size())+" sketches via SMM.");}
+		return sketches;
+	}
+	private ArrayList<Sketch> loadSketchesFromSketchFile(final FileFormat ff, boolean allowZeroSizeSketch){
+		boolean A48=(Sketch.CODING==Sketch.A48), HEX=(Sketch.CODING==Sketch.HEX), NUC=false, delta=true, counts=false, unsorted=false;
+		if(verbose2){System.err.println("Loading sketches from text.");}
+		ArrayList<Sketch> sketches=new ArrayList<Sketch>();
+		ByteFile bf=ByteFile.makeByteFile(ff);
+		int currentSketchSize=stTargetSketchSize;
+		int taxID=-1;
+		long spid=-1;
+		long imgID=-1;
+		long genomeSizeBases=0, genomeSizeKmers=0, genomeSequences=0;
+		long[] baseCounts=null;
+		byte[] r16S=null;
+		byte[] r18S=null;
+		int r16SLen=0;
+		int r18SLen=0;
+		float probCorrect=-1;
+		String name=null, name0=null, fname=ff.simpleName();
+		LongList list=null;
+		IntList countList=null;
+		ArrayList<String> meta=null;
+		long sum=0;
+		byte[] lastHeader=null;
+		for(byte[] line=bf.nextLine(); line!=null; line=bf.nextLine()){
+			if(line.length>0){
+				//				System.err.println("Processing line "+new String(line));
+				if(line[0]=='#'){
+					if(r16SLen>0 || r18SLen>0){
+						byte[] ssu=KillSwitch.copyOfRange(line, 5, line.length);
+						if(Tools.startsWith(line, "#16S:") || Tools.startsWith(line, "#SSU:")){
+							assert(r16SLen>0);
+							assert(ssu.length==r16SLen) : r16SLen+", "+line.length+"\n"+new String(line)+"\n";
+							r16S=ssu;
+							r16SLen=0;
+						}else if(Tools.startsWith(line, "#18S:")){
+							assert(r18SLen>0);
+							assert(ssu.length==r18SLen) : r18SLen+", "+line.length+"\n"+new String(line)+"\n";
+							r18S=ssu;
+							r18SLen=0;
+						}else{
+							assert(false) : new String(line);
+						}
+					}else{
+						lastHeader=line;
+						if(list!=null){
+							assert(list.size==list.array.length);
+							if(NUC || unsorted){
+								list.sort();
+								list.shrinkToUnique();
+							}else{
+								list.shrink();
+							}
+							if(list.size()>0 || allowZeroSizeSketch){
+								int[] keyCounts=countList==null ? null : countList.array;
+								Sketch sketch=new Sketch(list.array, keyCounts, baseCounts, r16S, r18S, taxID, imgID,
+										genomeSizeBases, genomeSizeKmers, genomeSequences, probCorrect, name, name0, fname, meta);
+								sketch.spid=spid;
+								sketches.add(sketch);
+							}
+							//						System.err.println("Made sketch "+sketch);
+						}
+						name=name0=null;
+						fname=ff.simpleName();
+						list=null;
+						countList=null;
+						meta=null;
+						baseCounts=null;
+						r16S=null;
+						r18S=null;
+						r16SLen=0;
+						r18SLen=0;
+						sum=0;
+						taxID=-1;
+						imgID=-1;
+						genomeSizeBases=0;
+						genomeSizeKmers=0;
+						genomeSequences=0;
+						probCorrect=-1;
+						int k_sketch=defaultK;
+						int k2_sketch=0;
+						int hashVersion_sketch=1;
+						if(line.length>1){
+							String[] split=new String(line, 1, line.length-1).split("\t");
+							for(String s : split){
+								final int colon=s.indexOf(':');
+								final String sub=s.substring(colon+1);
+								if(s.startsWith("SZ:") || s.startsWith("SIZE:")){//Sketch length
+									currentSketchSize=Integer.parseInt(sub);
+								}else if(s.startsWith("CD:")){//Coding
+									A48=HEX=NUC=delta=counts=unsorted=false;
+									for(int i=0; i<sub.length(); i++){
+										char c=sub.charAt(i);
+										if(c=='A'){A48=true;}
+										else if(c=='H'){HEX=true;}
+										else if(c=='R'){A48=HEX=false;}
+										else if(c=='N'){NUC=true;}
+										else if(c=='D'){delta=true;}
+										else if(c=='C'){counts=true;}
+										else if(c=='U'){unsorted=true;}
+										else if(c=='M'){assert(aminoOrTranslate()) : "Amino sketch in non-amino mode: "+new String(line);}
+										else if(c=='8'){assert(amino8) : "Amino8 sketch in non-amino8 mode: "+new String(line);}
+										else{assert(false) : "Unknown coding symbol: "+c+"\t"+new String(line);}
+									}
+								}else if(s.startsWith("K:")){//Kmer length
+									if(sub.indexOf(',')>=0){
+										String[] subsplit=sub.split(",");
+										assert(subsplit.length==2) : "Bad header component "+s;
+										int x=Integer.parseInt(subsplit[0]);
+										int y=Integer.parseInt(subsplit[1]);
+										k_sketch=Tools.max(x, y);
+										k2_sketch=Tools.min(x, y);
+									}else{
+										k_sketch=Integer.parseInt(sub);
+										k2_sketch=0;
+									}
+								}else if(s.startsWith("H:")){//Hash version
+									hashVersion_sketch=Integer.parseInt(sub);
+								}else if(s.startsWith("BC:") || s.startsWith("BASECOUNTS:")){//ACGTN
+									baseCounts=Parse.parseLongArray(sub);
+								}else if(s.startsWith("GS:") || s.startsWith("GSIZE:")){//Genomic bases
+									genomeSizeBases=Long.parseLong(sub);
+								}else if(s.startsWith("GK:") || s.startsWith("GKMERS:")){//Genomic kmers
+									genomeSizeKmers=Long.parseLong(sub);
+								}else if(s.startsWith("GQ:")){
+									genomeSequences=Long.parseLong(sub);
+								}else if(s.startsWith("GE:")){//Genome size estimate kmers
+									//ignore
+								}else if(s.startsWith("PC:")){//Probability of correctness
+									probCorrect=Float.parseFloat(sub);
+								}else if(s.startsWith("ID:") || s.startsWith("TAXID:")){
+									taxID=Integer.parseInt(sub);
+								}else if(s.startsWith("IMG:")){
+									imgID=Long.parseLong(sub);
+								}else if(s.startsWith("SPID:")){
+									spid=Integer.parseInt(sub);
+								}else if(s.startsWith("NM:") || s.startsWith("NAME:")){
+									name=sub;
+								}else if(s.startsWith("FN:")){
+									fname=sub;
+								}else if(s.startsWith("NM0:")){
+									name0=sub;
+								}else if(s.startsWith("MT_")){
+									if(meta==null){meta=new ArrayList<String>(1);}
+									meta.add(s.substring(3));
+								}else if(s.startsWith("16S:") || s.startsWith("SSU:")){
+									r16SLen=Integer.parseInt(sub);
+								}else if(s.startsWith("18S:")){
+									r18SLen=Integer.parseInt(sub);
+								}else{
+									assert(false) : "Unsupported header tag "+s;
+								}
+							}
+						}
+						if(KILL_OK){
+							if(k_sketch!=k && !NUC){KillSwitch.kill("Sketch kmer length "+k_sketch+
+									" differs from loaded kmer length "+k+"\n"+new String(line)+"\nfile: "+ff.name());}
+							if(k2_sketch!=k2 && !NUC){KillSwitch.kill("Sketch kmer length "+k_sketch+","+k2_sketch+
+									" differs from loaded kmer length "+k+","+k2+"\n"+new String(line)+"\nfile: "+ff.name());}
+							if(hashVersion_sketch!=HASH_VERSION && !NUC){KillSwitch.kill("Sketch hash version "+hashVersion_sketch+
+									" differs from loaded hash version "+HASH_VERSION+".\n"
+									+ "You may need to download the latest version of BBTools.\n"+new String(line)+"\nfile: "+ff.name());}
+						}else{//Potential hang
+							assert(k_sketch==k || NUC) : "Sketch kmer length "+k_sketch+" differs from loaded kmer length "+k+"\n"+new String(line);
+							assert(k2_sketch==k2 || NUC) : "Sketch kmer length "+k_sketch+","+k2_sketch+" differs from loaded kmer length "+k+","+k2+"\n"+new String(line);
+							assert(hashVersion_sketch==HASH_VERSION || NUC) : "Sketch hash version "+hashVersion_sketch+
+							" differs from loaded hash version "+HASH_VERSION+".\n"
+							+ "You may need to download the latest version of BBTools.\n"+new String(line)+"\n";
+						}
+						if(currentSketchSize>0 || allowZeroSizeSketch){
+							list=new LongList(Tools.max(1, currentSketchSize));
+							if(counts){countList=new IntList(Tools.max(1, currentSketchSize));}
+						}
+					}
+				}else{
+					long x=(counts ? Sketch.parseA48C(line, countList) : A48 ? Sketch.parseA48(line) :
+						HEX ? Sketch.parseHex(line) : NUC ? Sketch.parseNuc(line) : Parse.parseLong(line));
+//					System.err.println("sum="+sum+", x="+x+" -> "+(sum+x));
+					sum+=x;
+					assert(x>=0 || NUC) : "x="+x+"\nline="+new String(line)+"\nheader="+(lastHeader==null ? "null" : new String(lastHeader))+"\nlineNum="+bf.lineNum()+"\n";
+					assert(sum>=0 || !delta) : "The sketch was made with delta compression off.  Please regenerate it.";
+					assert(list!=null) : new String(line);
+					long key=(delta ? sum : x);
+					if(key>=0){list.add(key);}
+				}
+			}
+		}
+		if(list!=null && (list.size>0 || allowZeroSizeSketch)){
+			assert(list.size==list.array.length || NUC || unsorted || (allowZeroSizeSketch && list.size==0)) : list.size+"!="+list.array.length;
+			if(NUC || unsorted){
+				list.sort();
+				list.shrinkToUnique();
+			}else{
+				list.shrink();
+			}
+			int[] keyCounts=countList==null ? null : countList.array;
+			Sketch sketch=new Sketch(list.array, keyCounts, baseCounts, r16S, r18S, taxID, imgID,
+					genomeSizeBases, genomeSizeKmers, genomeSequences, probCorrect, name, name0, fname, meta);
+			sketch.spid=spid;
+			sketches.add(sketch);
+		}
+		if(verbose2){System.err.println("Loaded "+sketches.size()+" sketches from text.");}
+		return sketches;
+	}
+	/** Usually much faster due to not manifesting the multithreaded load Java slowdown.  Should incur less garbage collection also. */
+	private ArrayList<Sketch> loadSketchesFromSketchFile2(final FileFormat ff, boolean allowZeroSizeSketch){
+		boolean A48=(Sketch.CODING==Sketch.A48), HEX=(Sketch.CODING==Sketch.HEX), NUC=false, delta=true, counts=false, unsorted=false;
+		if(verbose2){System.err.println("Loading sketches from text.");}
+		ArrayList<Sketch> sketches=new ArrayList<Sketch>();
+		InputStream is=ReadWrite.getInputStream(ff.name(), BUFFERED_READER, false);
+		byte[] buffer=new byte[BUFLEN];
+		int start, limit=0;
+		try {
+			limit=is.read(buffer);
+		} catch (IOException e) {
+			KillSwitch.exceptionKill(e);
+		}
+		int currentSketchSize=stTargetSketchSize;
+		int taxID=-1;
+		long spid=-1;
+		long imgID=-1;
+		long genomeSizeBases=0, genomeSizeKmers=0, genomeSequences=0;
+		long[] baseCounts=null;
+		byte[] r16S=null;
+		byte[] r18S=null;
+		int r16SLen=0;
+		int r18SLen=0;
+		float probCorrect=-1;
+		String name=null, name0=null, fname=ff.simpleName();
+		LongList list=null;
+		IntList countList=null;
+		ArrayList<String> meta=null;
+		long sum=0;
+		byte[] lastHeader=null;
+		ByteBuilder bb=new ByteBuilder(256);
+		for(start=0; start<limit;){
+			//				System.err.println("Processing line "+new String(line));
+			if(buffer[start]=='#'){
+				bb.clear();
+				try {
+					while(buffer[start]!='\n'){
+						bb.append(buffer[start]);
+						start++;
+						if(start>=limit){start=0; limit=is.read(buffer);}
+					}
+				} catch (IOException e) {
+					KillSwitch.exceptionKill(e);
+				}
+				start++;
+				if(r16SLen>0 || r18SLen>0){
+					byte[] ssu=bb.toBytes(5, bb.length());
+					if(bb.startsWith("#16S:") || bb.startsWith("#SSU:")){
+						assert(r16SLen>0);
+						assert(ssu.length==r16SLen) : r16SLen+", "+bb.length+"\n"+bb+"\n";
+						r16S=ssu;
+						r16SLen=0;
+					}else if(bb.startsWith("#18S:")){
+						assert(r18SLen>0);
+						assert(ssu.length==r18SLen) : r18SLen+", "+bb.length+"\n"+bb+"\n";
+						r18S=ssu;
+						r18SLen=0;
+					}else{
+						assert(false) : bb;
+					}
+				}else{
+					//				byte[] line=lastHeader=bb.toBytes();
+					if(list!=null){
+						//This assertion fails sometimes for Silva per-sequence mode, but it's not important
+						//					assert(list.size==list.array.length) : list.size+", "+list.array.length+(lastHeader==null ? "" : ", "+new String(lastHeader));
+						if(NUC || unsorted){
+							list.sort();
+							list.shrinkToUnique();
+						}else{
+							list.shrink();
+						}
+						if(list.size()>0 || allowZeroSizeSketch){
+							int[] keyCounts=countList==null ? null : countList.array;
+							Sketch sketch=new Sketch(list.array, keyCounts, baseCounts, r16S, r18S, taxID, imgID,
+									genomeSizeBases, genomeSizeKmers, genomeSequences, probCorrect, name, name0, fname, meta);
+							sketch.spid=spid;
+							sketches.add(sketch);
+						}
+						//						System.err.println("Made sketch "+sketch);
+					}
+					name=name0=null;
+					fname=ff.simpleName();
+					list=null;
+					countList=null;
+					meta=null;
+					baseCounts=null;
+					r16S=null;
+					r18S=null;
+					r16SLen=0;
+					r18SLen=0;
+					sum=0;
+					taxID=-1;
+					imgID=-1;
+					genomeSizeBases=0;
+					genomeSizeKmers=0;
+					genomeSequences=0;
+					probCorrect=-1;
+					int k_sketch=defaultK;
+					int k2_sketch=0;
+					int hashVersion_sketch=1;
+					if(bb.length>1){
+						String[] split=new String(bb.array, 1, bb.length-1).split("\t");
+						for(String s : split){
+							final int colon=s.indexOf(':');
+							final String sub=s.substring(colon+1);
+							if(s.startsWith("SZ:") || s.startsWith("SIZE:")){//Sketch length
+								currentSketchSize=Integer.parseInt(sub);
+							}else if(s.startsWith("CD:")){//Coding
+								A48=HEX=NUC=delta=counts=unsorted=false;
+								for(int i=0; i<sub.length(); i++){
+									char c=sub.charAt(i);
+									if(c=='A'){A48=true;}
+									else if(c=='H'){HEX=true;}
+									else if(c=='R'){A48=HEX=false;}
+									else if(c=='N'){NUC=true;}
+									else if(c=='D'){delta=true;}
+									else if(c=='C'){counts=true;}
+									else if(c=='U'){unsorted=true;}
+									else if(c=='M'){assert(aminoOrTranslate()) : "Amino sketch in non-amino mode: "+bb;}
+									else if(c=='8'){assert(amino8) : "Amino8 sketch in non-amino8 mode: "+bb;}
+									else{assert(false) : "Unknown coding symbol: "+c+"\t"+bb;}
+								}
+							}else if(s.startsWith("K:")){//Kmer length
+								if(sub.indexOf(',')>=0){
+									String[] subsplit=sub.split(",");
+									assert(subsplit.length==2) : "Bad header component "+s;
+									int x=Integer.parseInt(subsplit[0]);
+									int y=Integer.parseInt(subsplit[1]);
+									k_sketch=Tools.max(x, y);
+									k2_sketch=Tools.min(x, y);
+								}else{
+									k_sketch=Integer.parseInt(sub);
+									k2_sketch=0;
+								}
+							}else if(s.startsWith("H:")){//Hash version
+								hashVersion_sketch=Integer.parseInt(sub);
+							}else if(s.startsWith("BC:") || s.startsWith("BASECOUNTS:")){//ACGTN
+								baseCounts=Parse.parseLongArray(sub);
+							}else if(s.startsWith("GS:") || s.startsWith("GSIZE:")){//Genomic bases
+								genomeSizeBases=Long.parseLong(sub);
+							}else if(s.startsWith("GK:") || s.startsWith("GKMERS:")){//Genomic kmers
+								genomeSizeKmers=Long.parseLong(sub);
+							}else if(s.startsWith("GQ:")){
+								genomeSequences=Long.parseLong(sub);
+							}else if(s.startsWith("GE:")){//Genome size estimate kmers
+								//ignore
+							}else if(s.startsWith("PC:")){//Probability of correctness
+								probCorrect=Float.parseFloat(sub);
+							}else if(s.startsWith("ID:") || s.startsWith("TAXID:")){
+								taxID=Integer.parseInt(sub);
+							}else if(s.startsWith("IMG:")){
+								imgID=Long.parseLong(sub);
+							}else if(s.startsWith("SPID:")){
+								spid=Integer.parseInt(sub);
+							}else if(s.startsWith("NM:") || s.startsWith("NAME:")){
+								name=sub;
+							}else if(s.startsWith("FN:")){
+								fname=sub;
+							}else if(s.startsWith("NM0:")){
+								name0=sub;
+							}else if(s.startsWith("MT_")){
+								if(meta==null){meta=new ArrayList<String>(1);}
+								meta.add(s.substring(3));
+							}else if(s.startsWith("16S:") || s.startsWith("SSU:")){
+								r16SLen=Integer.parseInt(sub);
+							}else if(s.startsWith("18S:")){
+								r18SLen=Integer.parseInt(sub);
+							}else{
+								assert(false) : "Unsupported header tag "+s;
+							}
+						}
+					}
+					if(KILL_OK){
+						if(k_sketch!=k && !NUC){KillSwitch.kill("Sketch kmer length "+k_sketch+
+								" differs from loaded kmer length "+k+"\n"+bb+"\nfile: "+ff.name());}
+						if(k2_sketch!=k2 && !NUC){KillSwitch.kill("Sketch kmer length "+k_sketch+","+k2_sketch+
+								" differs from loaded kmer length "+k+","+k2+"\n"+bb+"\nfile: "+ff.name());}
+						if(hashVersion_sketch!=HASH_VERSION && !NUC){KillSwitch.kill("Sketch hash version "+hashVersion_sketch+
+								" differs from loaded hash version "+HASH_VERSION+".\n"
+								+ "You may need to download the latest version of BBTools.\nfile: "+ff.name());}
+					}else{//Potential hang
+						assert(k_sketch==k || NUC) : "Sketch kmer length "+k_sketch+" differs from loaded kmer length "+k+"\n"+bb;
+						assert(k2_sketch==k2 || NUC) : "Sketch kmer length "+k_sketch+","+k2_sketch+" differs from loaded kmer length "+k+","+k2+"\n"+bb;
+						assert(hashVersion_sketch==HASH_VERSION || NUC) : "Sketch hash version "+hashVersion_sketch+
+						" differs from loaded hash version "+HASH_VERSION+".\n"
+						+ "You may need to download the latest version of BBTools.\nfile: "+ff.name();
+					}
+					if(currentSketchSize>0 || allowZeroSizeSketch){
+						list=new LongList(Tools.max(1, currentSketchSize));
+						if(counts){countList=new IntList(Tools.max(1, currentSketchSize));}
+					}
+				}
+			}else{
+				bb.clear();
+				try {
+					while(buffer[start]!='\n'){
+						bb.append(buffer[start]);
+						start++;
+						if(start>=limit){start=0; limit=is.read(buffer);}
+					}
+				} catch (IOException e) {
+					KillSwitch.exceptionKill(e);
+				}
+				start++;
+				long x=(counts ? Sketch.parseA48C(bb, countList) : A48 ? Sketch.parseA48(bb) :
+					HEX ? Sketch.parseHex(bb) : NUC ? Sketch.parseNuc(bb) : Parse.parseLong(bb.array, 0, bb.length));
+				//					System.err.println("sum="+sum+", x="+x+" -> "+(sum+x));
+				sum+=x;
+				assert(x>=0 || NUC) : "x="+x+"\nline="+bb+"\nheader="+(lastHeader==null ? "null" : new String(lastHeader))+"\n";
+				assert(sum>=0 || !delta) : "The sketch was made with delta compression off.  Please regenerate it.";
+				assert(list!=null) : bb;
+				long key=(delta ? sum : x);
+				if(key>=0){list.add(key);}
+			}
+			if(start>=limit){
+				start=0;
+				try {
+					limit=is.read(buffer);
+				} catch (IOException e) {
+					KillSwitch.exceptionKill(e);
+				}
+			}
+		}
+		if(list!=null && (list.size>0 || allowZeroSizeSketch)){
+			//This assertion fails sometimes for Silva per-sequence mode, but it's not important
+//			assert(list.size==list.array.length || NUC || unsorted || (allowZeroSizeSketch && list.size==0)) :
+//				list.size+"!="+list.array.length+(lastHeader==null ? "" : "\n"+new String(lastHeader));
+			if(NUC || unsorted){
+				list.sort();
+				list.shrinkToUnique();
+			}else{
+				list.shrink();
+			}
+			int[] keyCounts=countList==null ? null : countList.array;
+			Sketch sketch=new Sketch(list.array, keyCounts, baseCounts, r16S, r18S, taxID, imgID,
+					genomeSizeBases, genomeSizeKmers, genomeSequences, probCorrect, name, name0, fname, meta);
+			sketch.spid=spid;
+			sketches.add(sketch);
+		}
+		if(verbose2){System.err.println("Loaded "+sketches.size()+" sketches from text.");}
+		try {
+			is.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		return sketches;
+	}
+	/*--------------------------------------------------------------*/
+	public ArrayList<Sketch> loadSketchesFromString(String sketchString){
+		boolean A48=(Sketch.CODING==Sketch.A48), HEX=(Sketch.CODING==Sketch.HEX), NUC=false, delta=true, counts=false, unsorted=false;
+		ArrayList<Sketch> sketches=new ArrayList<Sketch>();
+		int currentSketchSize=stTargetSketchSize;
+		int taxID=-1;
+		long spid=-1;
+		long imgID=-1;
+		long genomeSizeBases=0, genomeSizeKmers=0, genomeSequences=0;
+		long[] baseCounts=null;
+		byte[] r16S=null;
+		byte[] r18S=null;
+		int r16SLen=0;
+		int r18SLen=0;
+		float probCorrect=-1;
+		String name=null, name0=null, fname=null;
+		LongList list=null;
+		IntList countList=null;
+		ArrayList<String> meta=null;
+		long sum=0;
+		String[] split0=sketchString.split("\n");
+		for(String line : split0){
+			if(line.length()>0){
+//				System.err.println("Processing line "+new String(line));
+				if(line.charAt(0)=='#'){
+					if(line.length()>1 && line.charAt(1)=='#'){
+						//ignore
+					}else if(r16SLen>0 || r18SLen>0){
+						byte[] ssu=KillSwitch.copyOfRange(line.getBytes(), 5, line.length());
+						if(line.startsWith("#16S:") || line.startsWith("#SSU:")){
+							assert(r16SLen>0);
+							assert(ssu.length==r16SLen) : r16SLen+", "+line.length()+"\n"+line+"\n";
+							r16S=ssu;
+							r16SLen=0;
+						}else if(line.startsWith("#18S:")){
+							assert(r18SLen>0);
+							assert(ssu.length==r18SLen) : r18SLen+", "+line.length()+"\n"+line+"\n";
+							r18S=ssu;
+							r18SLen=0;
+						}else{
+							assert(false) : line;
+						}
+					}else{
+						if(list!=null){
+							assert(list.size==list.array.length);
+							if(NUC || unsorted){
+								list.sort();
+								list.shrinkToUnique();
+							}else{
+								list.shrink();
+							}
+							if(list.size()>0){
+								int[] keyCounts=countList==null ? null : countList.array;
+								Sketch sketch=new Sketch(list.array, keyCounts, baseCounts, r16S, r18S, taxID, imgID,
+										genomeSizeBases, genomeSizeKmers, genomeSequences, probCorrect, name, name0, fname, meta);
+								sketch.spid=spid;
+								sketches.add(sketch);
+							}
+							//						System.err.println("Made sketch "+sketch);
+						}
+						name=name0=null;
+						fname=null;
+						list=null;
+						countList=null;
+						meta=null;
+						baseCounts=null;
+						r16S=null;
+						r18S=null;
+						r16SLen=0;
+						r18SLen=0;
+						sum=0;
+						taxID=-1;
+						imgID=-1;
+						genomeSizeBases=0;
+						genomeSizeKmers=0;
+						genomeSequences=0;
+						probCorrect=-1;
+						int k_sketch=defaultK;
+						int k2_sketch=0;
+						int hashVersion_sketch=1;
+						if(line.length()>1){
+							String[] split=line.substring(1).split("\t");
+							for(String s : split){
+								final int colon=s.indexOf(':');
+								final String sub=s.substring(colon+1);
+								if(s.startsWith("SZ:") || s.startsWith("SIZE:")){//Sketch length
+									currentSketchSize=Integer.parseInt(sub);
+								}else if(s.startsWith("CD:")){//Coding
+									A48=HEX=NUC=delta=counts=false;
+									for(int i=0; i<sub.length(); i++){
+										char c=sub.charAt(i);
+										if(c=='A'){A48=true;}
+										else if(c=='H'){HEX=true;}
+										else if(c=='R'){A48=HEX=false;}
+										else if(c=='N'){NUC=true;}
+										else if(c=='D'){delta=true;}
+										else if(c=='C'){counts=true;}
+										else if(c=='U'){unsorted=true;}
+										else if(c=='M'){assert(aminoOrTranslate()) : "Amino sketch in non-amino mode: "+new String(line);}
+										else if(c=='8'){assert(amino8) : "Amino8 sketch in non-amino8 mode: "+new String(line);}
+										else{assert(false) : "Unknown coding symbol: "+c+"\t"+new String(line);}
+									}
+								}else if(s.startsWith("K:")){//Kmer length
+									if(sub.indexOf(',')>=0){
+										String[] subsplit=sub.split(",");
+										assert(subsplit.length==2) : "Bad header component "+s;
+										int x=Integer.parseInt(subsplit[0]);
+										int y=Integer.parseInt(subsplit[1]);
+										k_sketch=Tools.max(x, y);
+										k2_sketch=Tools.min(x, y);
+									}else{
+										k_sketch=Integer.parseInt(s);
+										k2_sketch=0;
+									}
+								}else if(s.startsWith("H:")){//Hash version
+									hashVersion_sketch=Integer.parseInt(sub);
+								}else if(s.startsWith("BC:") || s.startsWith("BASECOUNTS:")){//ACGTN
+									baseCounts=Parse.parseLongArray(sub);
+								}else if(s.startsWith("GS:") || s.startsWith("GSIZE:")){//Genomic bases
+									genomeSizeBases=Long.parseLong(sub);
+								}else if(s.startsWith("GK:") || s.startsWith("GKMERS:")){//Genomic kmers
+									genomeSizeKmers=Long.parseLong(sub);
+								}else if(s.startsWith("GQ:")){
+									genomeSequences=Long.parseLong(sub);
+								}else if(s.startsWith("GE:")){//Genome size estimate kmers
+									//ignore
+								}else if(s.startsWith("PC:")){//Probability of correctness
+									probCorrect=Float.parseFloat(sub);
+								}else if(s.startsWith("ID:") || s.startsWith("TAXID:")){
+									taxID=Integer.parseInt(sub);
+								}else if(s.startsWith("IMG:")){
+									imgID=Long.parseLong(sub);
+								}else if(s.startsWith("SPID:")){
+									spid=Integer.parseInt(sub);
+								}else if(s.startsWith("NM:") || s.startsWith("NAME:")){
+									name=sub;
+								}else if(s.startsWith("FN:")){
+									fname=sub;
+								}else if(s.startsWith("NM0:")){
+									name0=sub;
+								}else if(s.startsWith("MT_")){
+									if(meta==null){meta=new ArrayList<String>(1);}
+									meta.add(s.substring(3));
+								}else if(s.startsWith("16S:") || s.startsWith("SSU:")){
+									r16SLen=Integer.parseInt(sub);
+								}else if(s.startsWith("18S:")){
+									r18SLen=Integer.parseInt(sub);
+								}else{
+									assert(false) : "Unsupported header tag "+s;
+								}
+							}
+						}
+						if(KILL_OK){
+							if(k_sketch!=k && !NUC){KillSwitch.kill("Sketch kmer length "+k_sketch+" differs from loaded kmer length "+k+"\n"+new String(line));}
+							if(k2_sketch!=k2 && !NUC){KillSwitch.kill("Sketch kmer length "+k_sketch+","+k2_sketch+" differs from loaded kmer length "+k+","+k2+"\n"+new String(line));}
+							if(hashVersion_sketch!=HASH_VERSION && !NUC){KillSwitch.kill("Sketch hash version "+hashVersion_sketch+
+									" differs from loaded hash version "+HASH_VERSION+".\n"
+											+ "You may need to download the latest version of BBTools.\n"+new String(line)+"\n");}
+						}else{//Potential hang
+							assert(k_sketch==k && !NUC) : "Sketch kmer length "+k_sketch+" differs from loaded kmer length "+k+"\n"+new String(line);
+							assert(k2_sketch==k2 && !NUC) : "Sketch kmer length "+k_sketch+","+k2_sketch+" differs from loaded kmer length "+k+","+k2+"\n"+new String(line);
+							assert(hashVersion_sketch==HASH_VERSION || NUC) : "Sketch hash version "+hashVersion_sketch+
+									" differs from loaded hash version "+HASH_VERSION+".\n"
+											+ "You may need to download the latest version of BBTools.\n"+new String(line)+"\n";
+						}
+						if(currentSketchSize>0){
+							list=new LongList(currentSketchSize);
+							if(counts){countList=new IntList(currentSketchSize);}
+						}
+					}
+				}else{
+					long x=(counts ? Sketch.parseA48C(line, countList) : A48 ? Sketch.parseA48(line) :
+						HEX ? Sketch.parseHex(line) : NUC ? Sketch.parseNuc(line) : Long.parseLong(line));
+//					System.err.println("sum="+sum+", x="+x+" -> "+(sum+x));
+					sum+=x;
+					assert(x>=0 || NUC) : x+"\n"+new String(line);
+					assert(sum>=0 || !delta) : "The sketch was made with delta compression off.  Please regenerate it.";
+					long key=(delta ? sum : x);
+					if(key>=0){list.add(key);}
+				}
+			}
+		}
+		if(list!=null){
+			assert(list.size==list.array.length || list.size()==0 || NUC || unsorted);
+			if(NUC || unsorted){
+				list.sort();
+				list.shrinkToUnique();
+			}else{
+				list.shrink();
+			}
+			int[] keyCounts=countList==null ? null : countList.array;
+			Sketch sketch=new Sketch(list.array, keyCounts, baseCounts, r16S, r18S, taxID, imgID,
+					genomeSizeBases, genomeSizeKmers, genomeSequences, probCorrect, name, name0, fname, meta);
+			sketch.spid=spid;
+			sketches.add(sketch);
+		}
+		return sketches;
+	}
+	/*--------------------------------------------------------------*/
+	/*----------------           Threads            ----------------*/
+	/*--------------------------------------------------------------*/
+	private class LoadThread extends Thread{
+		public LoadThread(ConcurrentLinkedQueue<StringNum> queue_, int mode_, float samplerate_, long reads_, float minEntropy, float minProb, byte minQual) {
+			queue=queue_;
+			list=new ArrayList<Sketch>();
+			smm=new SketchMakerMini(SketchTool.this, mode_, minEntropy, minProb, minQual);
+			samplerate=samplerate_;
+			reads=reads_;
+		}
+		@Override
+		public void run(){
+			success=false;
+			for(StringNum sn=queue.poll(); sn!=null; sn=queue.poll()){
+				ArrayList<Sketch> temp=null;
+				try {
+					temp=loadSketchesFromFile(sn.s, smm, 1, reads, smm.mode, samplerate, smm.minEntropy(), smm.minProb(), smm.minQual(), false);
+				} catch (Throwable e) {
+					System.err.println("Failure loading "+sn+":\n"+e);
+					e.printStackTrace();
+					success=false;
+				}
+				if(temp!=null && temp.size()>0){
+					if(smm.mode==PER_FILE){
+//						assert(temp.size()==1) : temp.size();
+						temp.get(0).sketchID=(int)sn.n;
+					}
+					for(Sketch s : temp){add(s);}
+				}
+			}
+			success=true;
+		}
+		private void add(Sketch s){
+			if(list!=null){
+				list.add(s);
+				return;
+			}
+			assert(false) : "Unsupported."; //The map logic is broken; needs to be synchronized.
+//			if(s.taxID<0){return;}
+////			assert(s.taxID>-1) : s.toHeader();
+//			TaxNode tn=tree.getNode(s.taxID);
+//			while(tn!=null && tn.pid!=tn.id && tn.level<taxLevel){
+//				TaxNode temp=tree.getNode(tn.pid);
+//				if(temp==null){break;}
+//				tn=temp;
+//			}
+//			if(tn==null){return;}
+//			Integer key=tn.id;
+//			Sketch old=map.get(key);
+//			if(old==null){
+//				s.taxID=key;
+//				map.put(key, s);
+//			}else{
+//				synchronized(old){
+//					old.add(s, maxLen);
+//				}
+//			}
+		}
+		final ConcurrentLinkedQueue<StringNum> queue;
+		ArrayList<Sketch> list;
+		boolean success=false;
+		final SketchMakerMini smm;
+		final float samplerate;
+		final long reads;
+//		ConcurrentHashMap<Integer, Sketch> map;
+	}
+	private class LoadThread2 extends Thread{
+		LoadThread2(ConcurrentReadInputStream cris_, float minEntropy, float minProb, byte minQual){
+			cris=cris_;
+			smm=new SketchMakerMini(SketchTool.this, ONE_SKETCH, minEntropy, minProb, minQual);
+		}
+		@Override
+		public void run(){
+			//Grab the first ListNum of reads
+			ListNum<Read> ln=cris.nextList();
+			//Grab the actual read list from the ListNum
+			ArrayList<Read> reads=(ln!=null ? ln.list : null);
+			//As long as there is a nonempty read list...
+			while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
+				//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;
+					if(validate){
+						if(r1!=null){r1.validate(true);}
+						if(r2!=null){r2.validate(true);}
+					}
+					smm.processReadPair(r1, r2);
+				}
+				//Notify the input stream that the list was used
+				cris.returnList(ln);
+				//Fetch a new list
+				ln=cris.nextList();
+				reads=(ln!=null ? ln.list : null);
+			}
+			//Notify the input stream that the final list was used
+			if(ln!=null){
+				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
+			}
+		}
+		private final boolean validate=!Read.VALIDATE_IN_CONSTRUCTOR;
+		ConcurrentReadInputStream cris;
+		SketchMakerMini smm;
+	}
+	/** Converts KmerTableSets to Heaps */
+	private class SketchThread extends Thread {
+		SketchThread(AtomicInteger next_, KmerTableSet kts_){
+			next=next_;
+			kts=kts_;
+		}
+		@Override
+		public void run(){
+			final int ways=kts.ways();
+			int tnum=next.getAndIncrement();
+			while(tnum<ways){
+				HashArray1D table=kts.getTable(tnum);
+				if(stTargetSketchSize>0){
+					if(heap==null){heap=new SketchHeap(stTargetSketchSize, minKeyOccuranceCount, trackCounts);}
+					toHeap(table, heap);
+				}else{
+					if(list==null){list=new LongList();}
+					toList(table, list);
+				}
+				tnum=next.getAndIncrement();
+			}
+		}
+		final AtomicInteger next;
+		final KmerTableSet kts;
+		SketchHeap heap;
+		LongList list;
+	}
+	/*--------------------------------------------------------------*/
+	/*----------------         Read Loading         ----------------*/
+	/*--------------------------------------------------------------*/
+	public Sketch processReadsMT(String fname, int maxThreads, long reads, int mode, float samplerate,
+			float minEntropy, float minProb, byte minQual, boolean allowZeroSizeSketch){
+		if(fname.indexOf('#')>=0 && FileFormat.isFastq(ReadWrite.rawExtension(fname)) && !new File(fname).exists()){
+			return processReadsMT(fname.replaceFirst("#", "1"), fname.replaceFirst("#", "2"), maxThreads, reads, mode, samplerate,
+					minEntropy, minProb, minQual, allowZeroSizeSketch);
+		}else{
+			return processReadsMT(fname, null, maxThreads, reads, mode, samplerate, minEntropy, minProb, minQual, allowZeroSizeSketch);
+		}
+	}
+	public Sketch processReadsMT(String fname1, String fname2, int maxThreads, long reads, int mode, float samplerate,
+			float minEntropy, float minProb, byte minQual, boolean allowZeroSizeSketch){
+		final FileFormat ffin1=FileFormat.testInput(fname1, FileFormat.FASTQ, null, true, true);
+		final FileFormat ffin2=FileFormat.testInput(fname2, FileFormat.FASTQ, null, true, true);
+		return processReadsMT(ffin1, ffin2, maxThreads, reads, mode, samplerate, minEntropy, minProb, minQual, allowZeroSizeSketch);
+	}
+	public Sketch processReadsMT(FileFormat ffin1, FileFormat ffin2, int maxThreads, long reads, int mode, DisplayParams params, boolean allowZeroSizeSketch){
+		return processReadsMT(ffin1, ffin2, maxThreads, reads, mode, params.samplerate, params.minEntropy, params.minProb, params.minQual, allowZeroSizeSketch);
+	}
+	public Sketch processReadsMT(FileFormat ffin1, FileFormat ffin2, int maxThreads, long reads, int mode, float samplerate,
+			float minEntropy, float minProb, byte minQual, boolean allowZeroSizeSketch){
+		assert(mode==ONE_SKETCH || mode==PER_FILE);
+		final boolean compressed=ffin1.compressed();
+		maxThreads=Tools.mid(1, maxThreads, Shared.threads());
+		//Create a read input stream
+		final ConcurrentReadInputStream cris;
+		String simpleName;
+		{
+			simpleName=ffin1.simpleName();
+			cris=ConcurrentReadInputStream.getReadInputStream(reads, true, ffin1, ffin2, null, null);
+			if(samplerate!=1){cris.setSampleRate(samplerate, sampleseed);}
+			cris.start(); //Start the stream
+//			if(verbose){outstream.println("Started cris");}
+		}
+		//TODO: bgzip actually decompresses fast.
+		final int threads=(int)Tools.min(maxThreads,
+				1.75f*(compressed ? 1 : 2)*(ffin2==null ? 4 : 8)*(mergePairs ? 3 : minEntropy>0 ? 2 : 1));
+		if(verbose2){System.err.println("Starting "+threads+" load threads.");}
+		ArrayList<LoadThread2> list=new ArrayList<LoadThread2>(threads);
+		for(int i=0; i<threads; i++){
+			list.add(new LoadThread2(cris, minEntropy, minProb, minQual));
+			list.get(i).start();
+		}
+		ArrayList<SketchHeap> heaps=new ArrayList<SketchHeap>(threads);
+		for(LoadThread2 pt : list){
+			//Wait until this thread has terminated
+			while(pt.getState()!=Thread.State.TERMINATED){
+				try {
+					//Attempt a join operation
+					pt.join();
+				} catch (InterruptedException e) {
+					//Potentially handle this, if it is expected to occur
+					e.printStackTrace();
+				}
+			}
+			if(pt.smm.heap!=null && pt.smm.heap.size()>0){
+				heaps.add(pt.smm.heap);
+			}
+		}
+		list.clear();
+		ReadWrite.closeStream(cris);
+		if(verbose2){System.err.println("Generating a sketch by combining thread output.");}
+		Sketch sketch=toSketch(heaps, allowZeroSizeSketch);
+		if(verbose2){System.err.println("Resulting sketch: "+((sketch==null) ? "null" : "length="+sketch.length()));}
+		if(sketch!=null){sketch.setFname(simpleName);}
+		return sketch;
+	}
+	/*--------------------------------------------------------------*/
+	/*----------------           Writing            ----------------*/
+	/*--------------------------------------------------------------*/
+	public static boolean write(ArrayList<Sketch> sketches, FileFormat ff[]){
+		final int len=ff.length;
+		ByteStreamWriter tsw[]=new ByteStreamWriter[len];
+		for(int i=0; i<len; i++){
+			tsw[i]=new ByteStreamWriter(ff[i]);
+			tsw[i].start();
+		}
+		boolean error=false;
+		for(int i=0; i<sketches.size(); i++){
+			write(sketches.get(i), tsw[i%len], new ByteBuilder());
+		}
+		for(int i=0; i<len; i++){
+			error|=tsw[i].poisonAndWait();
+		}
+		return error;
+	}
+	public static boolean write(ArrayList<Sketch> sketches, FileFormat ff){
+		final ByteStreamWriter tsw=new ByteStreamWriter(ff);
+		final ByteBuilder bb=new ByteBuilder();
+		tsw.start();
+		for(Sketch sketch : sketches){
+			write(sketch, tsw, bb);
+		}
+		return tsw.poisonAndWait();
+	}
+	public static boolean write(Sketch sketch, FileFormat ff){
+//		System.err.println(ff.name()+", "+new File(ff.name()).exists());
+		ByteStreamWriter tsw=new ByteStreamWriter(ff);
+//		assert(false) : new File(ff.name()).exists();
+		tsw.start();
+		write(sketch, tsw, null);
+		return tsw.poisonAndWait();
+	}
+	public static void write(Sketch sketch, ByteStreamWriter tsw, ByteBuilder bb){
+		if(bb==null){bb=new ByteBuilder();}
+		else{bb.clear();}
+		sketch.toBytes(bb);
+		tsw.print(bb);
+	}
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+//	final EntropyTracker eTracker;
+	final int stTargetSketchSize;
+	public final int minKeyOccuranceCount;
+	/** Force kmer counts to be tracked. */
+	public final boolean trackCounts;
+	/** Merge reads before processing kmers. */
+	public final boolean mergePairs;
+	public static int BUFLEN=16384;
+	public static boolean BUFFERED_READER=false;
+	/*--------------------------------------------------------------*/
+	/*----------------        Static Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+//	public static boolean verbose=false;
+}

Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/SketchTool.java @ 68:5028fdace37b