--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/tax/SplitByTaxa.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,388 @@
+package tax;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+import fileIO.ByteFile;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import shared.Parse;
+import shared.Parser;
+import shared.PreParser;
+import shared.ReadStats;
+import shared.Shared;
+import shared.Timer;
+import shared.Tools;
+import stream.ConcurrentReadInputStream;
+import stream.ConcurrentReadOutputStream;
+import stream.FASTQ;
+import stream.FastaReadInputStream;
+import stream.Read;
+import structures.ListNum;
+
+/**
+ * Filters sequences according to their taxonomy,
+ * as determined by the sequence name.  Sequences should
+ * be labeled with a gi number or NCBI taxID.
+ * 
+ * @author Brian Bushnell
+ * @date November 23, 2015
+ *
+ */
+public class SplitByTaxa {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Code entrance from the command line.
+	 * @param args Command line arguments
+	 */
+	public static void main(String[] args){
+		Timer t=new Timer();
+		SplitByTaxa x=new SplitByTaxa(args);
+		x.process(t);
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+	}
+	
+	/**
+	 * Constructor.
+	 * @param args Command line arguments
+	 */
+	public SplitByTaxa(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, getClass(), false);
+			args=pp.args;
+			outstream=pp.outstream;
+		}
+		
+		//Set some shared static variables
+		Shared.capBuffers(4);
+		ReadWrite.USE_UNPIGZ=true;
+		ReadWrite.USE_PIGZ=false;
+		ReadWrite.USE_GZIP=false;
+		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
+
+		boolean setInterleaved=false; //Whether interleaved was explicitly set.
+		String giTableFile=null;
+		String taxTreeFile=null;
+		
+		//Create a parser object
+		Parser parser=new Parser();
+		
+		//Parse each argument
+		for(int i=0; i<args.length; i++){
+			String arg=args[i];
+			
+			//Break arguments into their constituent parts, in the form of "a=b"
+			String[] split=arg.split("=");
+			String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+			
+			if(parser.parse(arg, a, b)){//Parse standard flags in the parser
+				//do nothing
+			}else if(a.equals("verbose")){
+				verbose=Parse.parseBoolean(b);
+			}else if(a.equals("taxlevel") || a.equals("tl") || a.equals("level") || a.equals("lv")){
+				taxLevelE=TaxTree.parseLevelExtended(b);
+			}else if(a.equals("table") || a.equals("gi") || a.equals("gitable")){
+				giTableFile=b;
+			}else if(a.equals("tree") || a.equals("taxtree")){
+				taxTreeFile=b;
+			}else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+				//				throw new RuntimeException("Unknown parameter "+args[i]);
+			}
+		}
+		
+		if("auto".equalsIgnoreCase(taxTreeFile)){taxTreeFile=TaxTree.defaultTreeFile();}
+		if("auto".equalsIgnoreCase(giTableFile)){giTableFile=TaxTree.defaultTableFile();}
+		
+		{//Process parser fields
+			Parser.processQuality();
+			
+			maxReads=parser.maxReads;
+			
+			overwrite=ReadStats.overwrite=parser.overwrite;
+			append=ReadStats.append=parser.append;
+			setInterleaved=parser.setInterleaved;
+			
+			in1=parser.in1;
+			in2=parser.in2;
+
+			out1=parser.out1;
+			out2=parser.out2;
+			
+			extin=parser.extin;
+			extout=parser.extout;
+		}
+		
+		//Do input file # replacement
+		if(in1!=null && in2==null && in1.indexOf('#')>-1 && !new File(in1).exists()){
+			in2=in1.replace("#", "2");
+			in1=in1.replace("#", "1");
+		}
+		
+		//Do output file # replacement
+		if(out1!=null && out2==null && out1.indexOf('#')>-1){
+			out2=out1.replace("#", "2");
+			out1=out1.replace("#", "1");
+		}
+		
+		assert(out1==null || out1.contains("%")) : "Output filename must contain % symbol.";
+		assert(out2==null || out2.contains("%")) : "Output filename must contain % symbol.";
+		assert(taxTreeFile!=null) : "This requires a taxtree file.  On NERSC systems, set tree=auto.";
+		
+		//Adjust interleaved detection based on the number of input files
+		if(in2!=null){
+			if(FASTQ.FORCE_INTERLEAVED){outstream.println("Reset INTERLEAVED to false because paired input files were specified.");}
+			FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
+		}
+		
+		assert(FastaReadInputStream.settingsOK());
+		
+		//Ensure there is an input file
+		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
+		
+		//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;
+		}
+		
+		//Ensure out2 is not set without out1
+		if(out1==null && out2!=null){throw new RuntimeException("Error - cannot define out2 without defining out1.");}
+		
+		//Adjust interleaved settings based on number of output files
+		if(!setInterleaved){
+			assert(in1!=null && (out1!=null || out2==null)) : "\nin1="+in1+"\nin2="+in2+"\nout1="+out1+"\nout2="+out2+"\n";
+			if(in2!=null){ //If there are 2 input streams.
+				FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
+				outstream.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
+			}else{ //There is one input stream.
+				if(out2!=null){
+					FASTQ.FORCE_INTERLEAVED=true;
+					FASTQ.TEST_INTERLEAVED=false;
+					outstream.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
+				}
+			}
+		}
+		
+		//Ensure output files can be written
+		if(!Tools.testOutputFiles(overwrite, append, false, out1, out2)){
+			outstream.println((out1==null)+", "+(out2==null)+", "+out1+", "+out2);
+			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+", "+out2+"\n");
+		}
+		
+		//Ensure input files can be read
+		if(!Tools.testInputFiles(false, true, in1, in2)){
+			throw new RuntimeException("\nCan't read some input files.\n");  
+		}
+		
+		//Ensure that no file was specified multiple times
+		if(!Tools.testForDuplicateFiles(true, in1, in2, out1, out2)){
+			throw new RuntimeException("\nSome file names were specified multiple times.\n");
+		}
+
+		//Create input FileFormat objects
+		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
+		ffin2=FileFormat.testInput(in2, FileFormat.FASTQ, extin, true, true);
+		
+		TaxFilter.loadGiTable(giTableFile);
+		tree=TaxFilter.loadTree(taxTreeFile);
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Create read streams and process all data */
+	public void process(Timer t){
+		
+		//Create a read input stream
+		final ConcurrentReadInputStream cris;
+		{
+			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, null, null);
+			cris.start(); //Start the stream
+			if(verbose){outstream.println("Started cris");}
+		}
+		boolean paired=cris.paired();
+		if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
+		
+		//Reset counters
+		readsProcessed=0;
+		basesProcessed=0;
+		
+		final HashMap<String, ConcurrentReadOutputStream> map=new HashMap<String, ConcurrentReadOutputStream>();
+		
+		//Process the read stream
+		processInner(cris, map);
+		
+		if(verbose){outstream.println("Finished; closing streams.");}
+		
+		//Write anything that was accumulated by ReadStats
+		errorState|=ReadStats.writeAll();
+		//Close the read streams
+		errorState|=ReadWrite.closeStream(cris);
+		
+		for(ConcurrentReadOutputStream ros : map.values()){
+			ReadWrite.closeStream(ros);
+		}
+		
+		//Report timing and results
+		t.stop();
+		outstream.println("Reads In:               \t"+readsProcessed+" reads       \t"+basesProcessed+" bases");
+		outstream.println();
+		outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
+		
+		//Throw an exception of there was an error in a thread
+		if(errorState){
+			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
+		}
+	}
+	
+	/** Iterate through the reads */
+	void processInner(final ConcurrentReadInputStream cris, HashMap<String, ConcurrentReadOutputStream> map){
+		
+		{
+			//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);
+			
+			//Check to ensure pairing is as expected
+			if(reads!=null && !reads.isEmpty()){
+				Read r=reads.get(0);
+				assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired());
+			}
+			
+			//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
+				if(verbose){outstream.println("Fetched "+reads.size()+" reads.");}
+				
+				//Loop through each read in the list
+				for(int idx=0; idx<reads.size(); idx++){
+					final Read r1=reads.get(idx);
+					
+					//Track the initial length for statistics
+					final int initialLength1=r1.length();
+					final int initialLength2=(r1.mateLength());
+					
+					//Increment counters
+					readsProcessed+=r1.pairCount();
+					basesProcessed+=initialLength1+initialLength2;
+					
+					TaxNode tn=tree.parseNodeFromHeader(r1.id, true);
+					if(tn==null){tn=tree.getNodeByName(r1.id);}
+					if(tn==null){tn=unknown;}
+					while(tn.levelExtended<taxLevelE && tn.id!=tn.pid){tn=tree.getNode(tn.pid);}
+					
+					if(out1!=null){
+						ConcurrentReadOutputStream ros=map.get(tn.name);
+						if(ros==null){
+							final int buff=4;
+							FileFormat ffout1=null, ffout2=null;
+							ffout1=FileFormat.testOutput(out1.replaceFirst("%", tn.name.replaceAll("\\s+", "_").replaceAll("[/\\\\]", "")), FileFormat.FASTQ, extout, false, overwrite, append, false);
+							if(out2!=null){ffout2=FileFormat.testOutput(out2.replaceFirst("%", tn.name.replaceAll("\\s+", "_").replaceAll("[/\\\\]", "")), FileFormat.FASTQ, extout, false, overwrite, append, false);}
+							ros=ConcurrentReadOutputStream.getStream(ffout1, ffout2, null, null, buff, null, false);
+							ros.start(); //Start the stream
+							map.put(tn.name, ros);
+						}
+						ArrayList<Read> temp=new ArrayList<Read>(1); //Kind of inefficient
+						temp.add(r1);
+						ros.add(temp, 0);
+					}
+				}
+				
+				//Notify the input stream that the list was used
+				cris.returnList(ln);
+				if(verbose){outstream.println("Returned a list.");}
+				
+				//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());
+			}
+		}
+		
+		//Do anything necessary after processing
+		
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary input file path */
+	private String in1=null;
+	/** Secondary input file path */
+	private String in2=null;
+
+	/** Primary output file path */
+	private String out1=null;
+	/** Secondary output file path */
+	private String out2=null;
+	
+	/** Override input file extension */
+	private String extin=null;
+	/** Override output file extension */
+	private String extout=null;
+	
+	/** The actual filter */
+	private int taxLevelE=TaxTree.stringToLevelExtended("phylum");
+	
+	/*--------------------------------------------------------------*/
+
+	/** Number of reads processed */
+	protected long readsProcessed=0;
+	/** Number of bases processed */
+	protected long basesProcessed=0;
+
+	/** Quit after processing this many input reads; -1 means no limit */
+	private long maxReads=-1;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary input file */
+	private final FileFormat ffin1;
+	/** Secondary input file */
+	private final FileFormat ffin2;
+	
+	private final TaxTree tree;
+	
+	private final TaxNode unknown=new TaxNode(-99, -99, TaxTree.LIFE, TaxTree.LIFE_E, "UNKNOWN");
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Common Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Print status messages to this output stream */
+	private PrintStream outstream=System.err;
+	/** Print verbose messages */
+	public static boolean verbose=false;
+	/** True if an error was encountered */
+	public boolean errorState=false;
+	/** Overwrite existing output files */
+	private boolean overwrite=false;
+	/** Append to existing output files */
+	private boolean append=false;
+	/** This flag has no effect on singlethreaded programs */
+	private final boolean ordered=false;
+	
+}