--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/AddSSU.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,548 @@
+package sketch;
+
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+
+import fileIO.ByteFile;
+import fileIO.ByteStreamWriter;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import shared.Parse;
+import shared.Parser;
+import shared.PreParser;
+import shared.Shared;
+import shared.Timer;
+import shared.Tools;
+import structures.ByteBuilder;
+import tax.TaxTree;
+
+/**
+ * @author Brian Bushnell
+ * @date May 9, 2016
+ *
+ */
+public class AddSSU {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        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
+		AddSSU x=new AddSSU(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 AddSSU(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, /*getClass()*/null, 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();
+		
+		{//Parse the arguments
+			final Parser parser=parse(args);
+			overwrite=parser.overwrite;
+			append=parser.append;
+			
+			in1=parser.in1;
+
+			out1=parser.out1;
+		}
+		
+		fixExtensions(); //Add or remove .gz or .bz2 as needed
+		checkFileExistence(); //Ensure files can be read and written
+		checkStatics(); //Adjust file-related static fields as needed for this program
+
+		ffout1=FileFormat.testOutput(out1, FileFormat.SKETCH, null, true, overwrite, append, false);
+		ffin1=FileFormat.testInput(in1, FileFormat.SKETCH, null, true, false);
+		
+		if(verbose){
+			System.err.println("Set r16SFile="+r16SFile);
+			System.err.println("Set r18SFile="+r18SFile);
+		}
+		
+		tree=(treeFile!=null && (preferSSUMapEuks || preferSSUMapProks || clear16SEuks || clear18SEuks || 
+				clear16SProks || clear18SProks || useSSUMapOnlyEuks || useSSUMapOnlyProks) ? TaxTree.loadTaxTree(treeFile, outstream, false, false) : null);
+		
+		if(preferSSUMapEuks || preferSSUMapProks || clear16SEuks || clear18SEuks || clear16SProks || clear18SProks || useSSUMapOnlyEuks || useSSUMapOnlyProks){
+			assert(tree!=null) : "preferSSUMapForEuks, clear16SEuks, and clear18SEuks require a TaxTree.";
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------    Initialization Helpers    ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Parse arguments from the command line */
+	private Parser parse(String[] args){
+		
+		Parser parser=new Parser();
+		for(int i=0; i<args.length; i++){
+			String arg=args[i];
+			String[] split=arg.split("=");
+			String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+			if(b!=null && b.equalsIgnoreCase("null")){b=null;}
+
+			if(a.equalsIgnoreCase("16S") || a.equalsIgnoreCase("16Sfile")){
+				r16SFile=b;
+			}else if(a.equalsIgnoreCase("18S") || a.equalsIgnoreCase("18Sfile")){
+				r18SFile=b;
+			}else if(a.equalsIgnoreCase("tree") || a.equalsIgnoreCase("treefile")){
+				treeFile=b;
+			}else if(a.equals("lines")){
+				maxLines=Long.parseLong(b);
+				if(maxLines<0){maxLines=Long.MAX_VALUE;}
+			}else if(a.equals("verbose")){
+				verbose=Parse.parseBoolean(b);
+//				ByteFile1.verbose=verbose;
+//				ByteFile2.verbose=verbose;
+//				ReadWrite.verbose=verbose;
+			}
+			
+			else if(a.equalsIgnoreCase("preferSSUMap")){
+				preferSSUMap=Parse.parseBoolean(b);
+			}else if(a.equalsIgnoreCase("preferSSUMapForEuks") || a.equalsIgnoreCase("preferSSUMapEuks")){
+				preferSSUMapEuks=Parse.parseBoolean(b);
+			}else if(a.equalsIgnoreCase("useSSUMapOnly")){
+				useSSUMapOnly=Parse.parseBoolean(b);
+			}else if(a.equalsIgnoreCase("useSSUMapOnlyEuks") || a.equalsIgnoreCase("SSUMapOnlyEuks")){
+				useSSUMapOnlyEuks=Parse.parseBoolean(b);
+			}else if(a.equalsIgnoreCase("useSSUMapOnlyProks") || a.equalsIgnoreCase("SSUMapOnlyProks")){
+				useSSUMapOnlyProks=Parse.parseBoolean(b);
+			}else if(a.equalsIgnoreCase("preferSSUMapForProks") || a.equalsIgnoreCase("preferSSUMapProks")){
+				preferSSUMapProks=Parse.parseBoolean(b);
+			}
+			
+			else if(a.equalsIgnoreCase("clearAll")){
+				clear16S=clear18S=Parse.parseBoolean(b);
+			}else if(a.equalsIgnoreCase("clear16S")){
+				clear16S=Parse.parseBoolean(b);
+			}else if(a.equalsIgnoreCase("clear18S")){
+				clear18S=Parse.parseBoolean(b);
+			}else if(a.equalsIgnoreCase("clear16SEuks")){
+				clear16SEuks=Parse.parseBoolean(b);
+			}else if(a.equalsIgnoreCase("clear18SEuks")){
+				clear18SEuks=Parse.parseBoolean(b);
+			}else if(a.equalsIgnoreCase("clear16SProks")){
+				clear16SProks=Parse.parseBoolean(b);
+			}else if(a.equalsIgnoreCase("clear18SProks")){
+				clear18SProks=Parse.parseBoolean(b);
+			}
+			
+			else if(parser.parse(arg, a, b)){
+				//do nothing
+			}else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+				//				throw new RuntimeException("Unknown parameter "+args[i]);
+			}
+		}
+		if("auto".equalsIgnoreCase(r16SFile)){r16SFile=TaxTree.default16SFile();}
+		if("auto".equalsIgnoreCase(r18SFile)){r18SFile=TaxTree.default18SFile();}
+		SSUMap.r16SFile=r16SFile;
+		SSUMap.r18SFile=r18SFile;
+		
+		return parser;
+	}
+	
+	/** Add or remove .gz or .bz2 as needed */
+	private void fixExtensions(){
+		in1=Tools.fixExtension(in1);
+		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
+	}
+	
+	/** 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 file "+out1+"\n");
+		}
+		
+		//Ensure input files can be read
+		if(!Tools.testInputFiles(false, true, in1, r16SFile, r18SFile)){
+			throw new RuntimeException("\nCan't read some input files.\n");  
+		}
+		assert(in1!=null) : "Input sketch file is required";
+		assert(r16SFile!=null || r18SFile!=null) : "Input SSU file is required";
+		
+		//Ensure that no file was specified multiple times
+		if(!Tools.testForDuplicateFiles(true, in1, out1, r16SFile, r18SFile)){
+			throw new RuntimeException("\nSome file names were specified multiple times.\n");
+		}
+	}
+	
+	/** 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;
+		}
+		
+//		if(!ByteFile.FORCE_MODE_BF2){
+//			ByteFile.FORCE_MODE_BF2=false;
+//			ByteFile.FORCE_MODE_BF1=true;
+//		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	void process(Timer t){
+		
+		ByteFile bf=ByteFile.makeByteFile(ffin1);
+		ByteStreamWriter bsw=makeBSW(ffout1);
+		
+		processInner(bf, bsw);
+		
+		errorState|=bf.close();
+		if(bsw!=null){errorState|=bsw.poisonAndWait();}
+		
+		t.stop();
+
+		outstream.println(Tools.timeLinesBytesProcessed(t, linesProcessed, bytesProcessed, 8));
+		outstream.println(Tools.linesBytesOut(linesProcessed, bytesProcessed, linesOut, bytesOut, 8, true));
+		
+		outstream.println();
+		outstream.println(Tools.number("Sketches:", sketchCount, 8));
+		outstream.println(Tools.number("16S In:", r16Sin, 8));
+		outstream.println(Tools.number("18S In:", r18Sin, 8));
+		outstream.println(Tools.number("16S Added:", r16SfromMap, 8));
+		outstream.println(Tools.number("18S Added:", r18SfromMap, 8));
+		outstream.println(Tools.numberPercent("16S Out:", r16Sout, r16Sout*100.0/sketchCount, 2, 8));
+		outstream.println(Tools.numberPercent("18S Out:", r18Sout, r18Sout*100.0/sketchCount, 2, 8));
+		
+		if(errorState){
+			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private static ByteStreamWriter makeBSW(FileFormat ff){
+		if(ff==null){return null;}
+		ByteStreamWriter bsw=new ByteStreamWriter(ff);
+		bsw.start();
+		return bsw;
+	}
+	
+//	private void processInner_old(ByteFile bf, ByteStreamWriter bsw){
+//		SSUMap.load(outstream);
+//		
+//		if(verbose){
+//			System.err.println("Loaded SSUMap; |16S|="+SSUMap.r16SCount()+", |18S|="+SSUMap.r18SCount());
+//		}
+//		
+//		byte[] line=bf.nextLine();
+////		ByteBuilder bb=new ByteBuilder();
+//
+//		final byte[] ssuBytes="SSU:".getBytes();
+//		final byte[] r16SBytes="16S:".getBytes();
+//		final byte[] r18SBytes="18S:".getBytes();
+//
+//		while(line!=null){
+//			if(line.length>0){
+//				if(maxLines>0 && linesProcessed>=maxLines){break;}
+//				linesProcessed++;
+//				bytesProcessed+=(line.length+1);
+//
+//				final boolean header=(line[0]=='#');
+//
+//				linesOut++;
+//				bytesOut+=(line.length+1);
+//
+//				if(header){
+//					if(Tools.startsWith(line, "#SZ:")){
+//						sketchCount++;
+//
+//						bsw.print(line);
+//
+//						final int tid=parseTaxID(line);
+//						final boolean has16S=Tools.contains(line, ssuBytes, 0) || Tools.contains(line, r16SBytes, 0);
+//						final boolean has18S=Tools.contains(line, r18SBytes, 0);
+//
+//						if(verbose){
+//							System.err.println("For line "+new String(line)+":");
+//							System.err.println("tid="+tid+", has16S="+has16S+", has18S="+has18S);
+//						}
+//
+//						if(tid>0){
+//							final byte[] r16S=has16S ? null : SSUMap.r16SMap.get(tid);
+//							final byte[] r18S=has18S ? null : SSUMap.r18SMap.get(tid);
+//							if(r16S!=null){bsw.print("\t16S:").print(r16S.length); ssuOut++;}
+//							if(r18S!=null){bsw.print("\t18S:").print(r18S.length); ssuOut++;}
+//							if(r16S!=null){bsw.print("\n#16S:").print(r16S);}
+//							if(r18S!=null){bsw.print("\n#18S:").print(r18S);}
+//
+//							if(verbose){System.err.println("Found 16S: "+(r16S!=null)+"; found 18S: "+(r18S!=null));}
+//						}
+//						bsw.println();
+//					}else if(Tools.startsWith(line, "#16S:") || Tools.startsWith(line, "#18S:") || Tools.startsWith(line, "#SSU:")){
+//						bsw.println(line);
+//						ssuIn++;
+//						ssuOut++;
+//					}else{
+//						assert(Tools.startsWith(line, "##")) : new String(line);
+//						bsw.println(line);
+//					}
+//				}else{
+//					bsw.println(line);
+//				}
+//			}
+//			line=bf.nextLine();
+//		}
+//	}
+	
+	private void processInner(ByteFile bf, ByteStreamWriter bsw){
+		SSUMap.load(outstream);
+		
+		if(verbose){
+			System.err.println("Loaded SSUMap; |16S|="+SSUMap.r16SCount()+", |18S|="+SSUMap.r18SCount());
+		}
+		
+		byte[] line=bf.nextLine();
+//		ByteBuilder bb=new ByteBuilder();
+
+//		final byte[] ssuBytes="SSU:".getBytes();
+//		final byte[] r16SBytes="16S:".getBytes();
+//		final byte[] r18SBytes="18S:".getBytes();
+
+		SketchHeader header=null;
+		while(line!=null){
+			if(line.length>0){
+				if(maxLines>0 && linesProcessed>=maxLines){break;}
+				linesProcessed++;
+				bytesProcessed+=(line.length+1);
+
+				final boolean isHeader=(line[0]=='#');
+
+				if(isHeader){
+					if(Tools.startsWith(line, "#SZ:")){
+						assert(header==null) : "\nReplacing this:\n"+header.toBytes()+"\nWith this:\n"+new String(line)+"\n";
+						header=new SketchHeader(line);
+						sketchCount++;
+					}else if(Tools.startsWith(line, "##")){
+						bsw.println(line);
+
+						linesOut++;
+						bytesOut+=(line.length+1);
+					}else{
+						header.addLine(line);
+					}
+				}else{
+					if(header!=null){
+						try {
+							processHeader(header);
+						} catch (Throwable e) {
+							e.printStackTrace();
+							assert(false) : header.toBytes();
+						}
+						r16Sout+=(header.r16S==null ? 0 : 1);
+						r18Sout+=(header.r18S==null ? 0 : 1);
+						linesOut+=1+(header.r16S==null ? 0 : 1)+(header.r18S==null ? 0 : 1);
+						ByteBuilder bb=header.toBytes();
+						bytesOut+=(bb.length+1);
+						bsw.println(bb);
+						header=null;
+					}
+					bsw.println(line);
+
+					linesOut++;
+					bytesOut+=(line.length+1);
+				}
+			}
+			line=bf.nextLine();
+		}
+	}
+	
+	void processHeader(SketchHeader header){
+		
+		if(verbose){System.err.println("Processing tid "+header.tid+":\n"+header.toBytes()+"\n");}
+
+		final boolean euk=(tree!=null && header.tid>0 && header.tid<SketchObject.minFakeID) ? tree.isEukaryote(header.tid) : false;
+		final boolean prok=(tree!=null && header.tid>0 && header.tid<SketchObject.minFakeID) ? tree.isProkaryote(header.tid) : false;
+		if(useSSUMapOnly || (useSSUMapOnlyEuks && euk) || (useSSUMapOnlyProks && prok)){header.r16S=header.r18S=null;}
+		if(header.tid>0){
+			final boolean preferMap=(preferSSUMap || (preferSSUMapEuks && euk) || (preferSSUMapProks && prok));
+			byte[] r16S=(SSUMap.r16SMap==null ? null : SSUMap.r16SMap.get(header.tid));
+			byte[] r18S=(SSUMap.r18SMap==null ? null : SSUMap.r18SMap.get(header.tid));
+			if(r16S!=null && (preferMap || header.r16S==null)){
+				header.r16S=r16S;
+				r16SfromMap++;
+			}
+			if(r18S!=null && (preferMap || header.r18S==null)){
+				header.r18S=r18S;
+				r18SfromMap++;
+			}
+		}
+		if(clear16S || (clear16SEuks && euk) || (clear16SProks && prok)){header.r16S=null;}
+		if(clear18S || (clear18SEuks && euk) || (clear18SProks && prok)){header.r18S=null;}
+	}
+	
+	int parseTaxID(byte[] line){
+		String[] split=Tools.tabPattern.split(new String(line));
+		for(String s : split){
+			if(s.startsWith("ID:") || s.startsWith("TAXID:")){
+				final int colon=s.indexOf(':');
+				final String sub=s.substring(colon+1);
+				return Integer.parseInt(sub);
+			}
+		}
+		return -1;
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	//A very limited parser
+	private class SketchHeader {
+		
+		SketchHeader(byte[] line){
+			this(new String(line, 1, line.length-1));
+		}
+		
+		SketchHeader(String line){
+			if(line.charAt(0)=='#'){line=line.substring(1);}
+			assert(line.startsWith("SZ:"));
+			String[] split=Tools.tabPattern.split(line);
+			fields=new ArrayList<String>(line.length()+2);
+			int tid_=-1;
+			for(String s : split){
+				if(s.startsWith("16S:") || s.startsWith("18S:") || s.startsWith("SSU:")){
+					//do nothing
+				}else{
+					if(s.startsWith("ID:") || s.startsWith("TAXID:")){
+						final int colon=s.indexOf(':');
+						final String sub=s.substring(colon+1);
+						tid_=Integer.parseInt(sub);
+					}
+					fields.add(s);
+				}
+			}
+			tid=tid_;
+		}
+		
+		void addLine(byte[] line){
+			assert(line[0]=='#');
+			assert(line[1]=='1' || line[1]=='S') : new String(line);
+			if(Tools.startsWith(line, "#16S:") || Tools.startsWith(line, "#SSU:")){
+				assert(r16S==null);
+				r16S=Arrays.copyOfRange(line, 5, line.length);
+				r16Sin++;
+			}else if(Tools.startsWith(line, "#18S:")){
+				assert(r18S==null);
+				r18S=Arrays.copyOfRange(line, 5, line.length);
+				r18Sin++;
+			}else{
+				assert(false) : new String(line);
+			}
+		}
+		
+		ByteBuilder toBytes(){
+			ByteBuilder bb=new ByteBuilder(1000);
+			bb.append('#');
+			for(int i=0; i<fields.size(); i++){
+				if(i>0){bb.tab();}
+				bb.append(fields.get(i));
+			}
+			if(r16S!=null){bb.tab().append("16S:").append(r16S.length);}
+			if(r18S!=null){bb.tab().append("18S:").append(r18S.length);}
+			
+			if(r16S!=null){bb.nl().append("#16S:").append(r16S);}
+			if(r18S!=null){bb.nl().append("#18S:").append(r18S);}
+			return bb;
+		}
+		
+		final int tid;
+		ArrayList<String> fields;
+		byte[] r16S;
+		byte[] r18S;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private String in1=null;
+	private String out1=null;
+	private String r16SFile="auto";
+	private String r18SFile="auto";
+	private String treeFile="auto";
+
+	boolean preferSSUMap=false;
+	boolean preferSSUMapEuks=false;
+	boolean preferSSUMapProks=false;
+	boolean useSSUMapOnly=false;
+	boolean useSSUMapOnlyEuks=false;
+	boolean useSSUMapOnlyProks=false;
+	boolean clear16S=false;
+	boolean clear18S=false;
+	boolean clear16SEuks=false;
+	boolean clear18SEuks=false;
+	boolean clear16SProks=false;
+	boolean clear18SProks=false;
+	
+	/*--------------------------------------------------------------*/
+	
+	private long linesProcessed=0;
+	private long linesOut=0;
+	private long bytesProcessed=0;
+	private long bytesOut=0;
+	
+	private long sketchCount=0;
+	
+	private long r16Sin=0;
+	private long r16Sout=0;
+	private long r16SfromMap=0;
+	private long r18Sin=0;
+	private long r18Sout=0;
+	private long r18SfromMap=0;
+	
+	private long maxLines=Long.MAX_VALUE;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private final FileFormat ffin1;
+	private final FileFormat ffout1;
+	
+	private final TaxTree tree;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Common Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private PrintStream outstream=System.err;
+	public static boolean verbose=false;
+	public boolean errorState=false;
+	private boolean overwrite=false;
+	private boolean append=false;
+	
+}