--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/InvertKey.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,316 @@
+package sketch;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.ArrayList;
+
+import dna.AminoAcid;
+import fileIO.ByteFile;
+import fileIO.ByteFile1;
+import fileIO.ByteFile2;
+import fileIO.ByteStreamWriter;
+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.ConcurrentGenericReadInputStream;
+import stream.ConcurrentReadInputStream;
+import stream.FASTQ;
+import stream.FastaReadInputStream;
+import stream.Read;
+import structures.ListNum;
+import structures.LongHashSet;
+
+/**
+ * @author Brian Bushnell
+ * @date Oct 17, 2014
+ *
+ */
+public class InvertKey extends SketchObject {
+	
+	public static void main(String[] args){
+		Timer t=new Timer();
+		InvertKey x=new InvertKey(args);
+		x.process(t);
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+	}
+	
+	public InvertKey(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, getClass(), false);
+			args=pp.args;
+			outstream=pp.outstream;
+		}
+		
+		Shared.capBuffers(4);
+		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
+		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
+		
+		FASTQ.TEST_INTERLEAVED=FASTQ.FORCE_INTERLEAVED=false;
+		int k_=32, k2_=0;
+		
+		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(a.equals("verbose")){
+				verbose=Parse.parseBoolean(b);
+				ByteFile1.verbose=verbose;
+				ByteFile2.verbose=verbose;
+				stream.FastaReadInputStream.verbose=verbose;
+				ConcurrentGenericReadInputStream.verbose=verbose;
+				stream.FastqReadInputStream.verbose=verbose;
+				ReadWrite.verbose=verbose;
+			}else if(a.equals("key")){
+				keyString=b;
+			}else if(a.equals("out")){
+				out1=b;
+			}else if(a.equalsIgnoreCase("k")){
+				assert(b!=null) : "Bad parameter: "+arg;
+				if(b.indexOf(',')>=0){
+					String[] bsplit=b.split(",");
+					assert(bsplit.length==2) : "Bad argument "+arg;
+					int x=Integer.parseInt(bsplit[0]);
+					int y=Integer.parseInt(bsplit[1]);
+					k_=Tools.max(x, y);
+					k2_=Tools.min(x, y);
+					if(k_==k2_){k2_=0;}
+				}else{
+					k_=Integer.parseInt(b);
+					k2_=0;
+				}
+			}else if(a.equalsIgnoreCase("printonce")){
+				printOnce=Parse.parseBoolean(b);
+			}else if(parser.in1==null && i==0 && !arg.contains("=") && (arg.toLowerCase().startsWith("stdin") || new File(arg).exists())){
+				parser.in1=arg;
+			}else if(parser.out1==null && i==1 && !arg.contains("=")){
+				out1=arg;
+			}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]);
+			}
+		}
+		
+		k=k_;
+		k2=k2_;
+		shift=2*k;
+		shift2=shift-2;
+		mask=(shift>63 ? -1L : ~((-1L)<<shift)); //Conditional allows K=32
+		
+		{//Process parser fields
+			Parser.processQuality();
+			
+			maxReads=parser.maxReads;
+			
+			overwrite=ReadStats.overwrite=parser.overwrite;
+			append=ReadStats.append=parser.append;
+			
+			in1=parser.in1;
+		}
+		
+		assert(FastaReadInputStream.settingsOK());
+		
+		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
+		if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2){
+			ByteFile.FORCE_MODE_BF2=false;
+			ByteFile.FORCE_MODE_BF1=true;
+		}
+
+		if(out1!=null && out1.equalsIgnoreCase("null")){out1=null;}
+		
+		if(!Tools.testOutputFiles(overwrite, append, false, out1)){
+			outstream.println((out1==null)+", "+out1);
+			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+"\n");
+		}
+		
+		ffout1=FileFormat.testOutput(out1, FileFormat.FASTA, null, true, overwrite, append, false);
+
+		ffin1=FileFormat.testInput(in1, FileFormat.FASTA, null, true, true);
+		
+		SketchObject.postParse();
+		
+		if(keyString.indexOf(',')>0){
+			String[] split=keyString.split(",");
+			set=new LongHashSet(split.length*2);
+			for(String s : split){
+				long x=Long.MAX_VALUE-Sketch.parseA48(s);
+				set.add(x);
+//				assert(set.contains(x)) : x+", "+set.size()+", "+set.toStringListView();
+			}
+			key0=-1;
+//			System.err.println(set.toStringListView()+", "+set.size());
+			assert(!set.isEmpty());
+		}else if(keyString.endsWith(".sketch")){
+			SketchTool tool=new SketchTool(10000, 0, false, false);
+			Sketch sk=tool.loadSketchesFromFile(keyString, null, 0, 1000000, SketchObject.ONE_SKETCH, 1f, 0f, 0f, (byte)0, false).get(0);
+			set=new LongHashSet(sk.length()*2);
+			for(long x : sk.keys){set.add(Long.MAX_VALUE-x);}
+			key0=-1;
+//			System.err.println(set.toStringListView()+", "+set.size());
+			assert(!set.isEmpty());
+		}else{
+			key0=Long.MAX_VALUE-Sketch.parseA48(keyString);
+			set=null;
+//			System.err.println(key0);
+		}
+	}
+	
+	void process(Timer t){
+		
+		final ConcurrentReadInputStream cris;
+		{
+			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, null, null);
+			cris.start();
+			if(verbose){outstream.println("Started cris");}
+		}
+		boolean paired=cris.paired();
+//		if(verbose){
+			if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
+//		}
+
+		final ByteStreamWriter bsw;
+		if(out1!=null){
+			fasta=ffout1.fasta() && !out1.endsWith(".txt");
+			bsw=new ByteStreamWriter(ffout1);
+			bsw.start();
+		}else{bsw=null;}
+		
+		long readsProcessed=0;
+		long basesProcessed=0;
+		boolean finished=false;
+		
+		{
+			
+			ListNum<Read> ln=cris.nextList();
+			ArrayList<Read> reads=(ln!=null ? ln.list : null);
+			
+//			outstream.println("Fetched "+reads);
+			
+			if(reads!=null && !reads.isEmpty()){
+				Read r=reads.get(0);
+				assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired());
+			}
+			
+			while(reads!=null && reads.size()>0 && !finished){
+				
+				for(int idx=0; idx<reads.size() && !finished; idx++){
+					final Read r1=reads.get(idx);
+
+					finished=invert(key0, r1, bsw);
+					
+					final int initialLength1=r1.length();
+					
+					readsProcessed++;
+					basesProcessed+=initialLength1;
+				}
+
+				cris.returnList(ln);
+				ln=cris.nextList();
+				reads=(ln!=null ? ln.list : null);
+			}
+			if(ln!=null){
+				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
+			}
+		}
+		
+		errorState|=(ReadWrite.closeStream(cris));
+		if(bsw!=null){errorState|=bsw.poisonAndWait();}
+		
+		t.stop();
+		outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
+		
+		if(errorState && !finished && maxReads<1){
+			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
+		}
+	}
+	
+	private boolean invert(long key2, Read r, ByteStreamWriter bsw) {
+		final byte[] bases=r.bases;
+		
+		long kmer=0;
+		long rkmer=0;
+		int len=0;
+		
+
+//		System.err.println("Looking for "+key+"\t"+Sketch.toA48(key)+"\t"+Sketch.toA48(Long.MAX_VALUE-key));
+		
+		for(int i=0; i<bases.length; i++){
+			byte b=bases[i];
+			long x=AminoAcid.baseToNumber[b];
+			long x2=AminoAcid.baseToComplementNumber[b];
+			kmer=((kmer<<2)|x)&mask;
+			rkmer=((rkmer>>>2)|(x2<<shift2))&mask;
+			if(x<0){len=0; rkmer=0;}else{len++;}
+			if(len>=k){
+				kmersProcessed++;
+				final long hashcode=hash(kmer, rkmer);
+				boolean found=(key0>=0 ? hashcode==key0 : set.contains(hashcode));
+				if(found){
+					if(fasta){bsw.println(">"+Sketch.toA48(Long.MAX_VALUE-hashcode)+" "+(i-k+1)+" "+r.id);}
+					bsw.println(AminoAcid.kmerToString(Tools.min(kmer, rkmer), k));
+					if(printOnce){
+						if(key0>=0){return true;}
+						else{
+							set.remove(hashcode);
+							return set.isEmpty();
+						}
+					}
+				}
+			}
+		}
+		return false;
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	final long key0;
+	final LongHashSet set;
+	
+	final int shift;
+	final int shift2;
+	final long mask;
+	
+	boolean printOnce=true;
+	long kmersProcessed=0;
+	
+	private String in1=null;
+	boolean fasta;
+	boolean sketch;
+	private String keyString=null;
+
+	private String out1="stdout.fa";
+	
+	/*--------------------------------------------------------------*/
+
+	private long maxReads=-1;
+	
+	/*--------------------------------------------------------------*/
+	
+	private final FileFormat ffin1;
+
+	private final FileFormat ffout1;
+	
+	
+	/*--------------------------------------------------------------*/
+	
+	private PrintStream outstream=System.err;
+	public static boolean verbose=false;
+	public boolean errorState=false;
+	private boolean overwrite=false;
+	private boolean append=false;
+	
+}