--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/SSUMap.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,107 @@
+package sketch;
+
+import java.io.PrintStream;
+import java.util.HashMap;
+
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import shared.Shared;
+import stream.ConcurrentReadInputStream;
+import stream.FASTQ;
+import stream.Read;
+import structures.ListNum;
+import tax.GiToTaxid;
+import tax.TaxTree;
+
+public class SSUMap {
+	
+	public static synchronized void load(PrintStream outstream){
+		if(r16SFile!=null && r16SMap==null){
+			r16SMap=load(r16SFile, TaxTree.default16SFile(), outstream);
+		}
+		if(r18SFile!=null && r18SMap==null){
+			r18SMap=load(r18SFile, TaxTree.default18SFile(), outstream);
+		}
+	}
+	
+	private static synchronized HashMap<Integer, byte[]> load(String ssuFile, String defaultFile, PrintStream outstream){
+		HashMap<Integer, byte[]> map=null;
+		if(ssuFile!=null){
+			final boolean oldAminoIn=Shared.AMINO_IN;
+			final boolean oldInterleaved=FASTQ.FORCE_INTERLEAVED;
+			Shared.AMINO_IN=false;//SSUs are nucleotide, which can cause a crash, esp. with IUPAC symbols
+			FASTQ.FORCE_INTERLEAVED=false;
+
+			String fname=ssuFile;
+			if("auto".equalsIgnoreCase(fname)){fname=defaultFile;}
+			final FileFormat ffssu=FileFormat.testInput(fname, FileFormat.FA, null, true, false);
+			map=loadSSU(ffssu, outstream);
+
+			Shared.AMINO_IN=oldAminoIn;
+			FASTQ.FORCE_INTERLEAVED=oldInterleaved;
+		}
+		return map;
+	}
+	
+	private static HashMap<Integer, byte[]> loadSSU(FileFormat ff, PrintStream outstream){
+		ConcurrentReadInputStream cris=makeCris(ff, outstream);
+		HashMap<Integer, byte[]> map=new HashMap<Integer, byte[]>(1000000);
+		
+		//Grab the first ListNum of reads
+		ListNum<Read> ln=cris.nextList();
+
+		//Check to ensure pairing is as expected
+		if(ln!=null && !ln.isEmpty()){
+//			if(verbose){outstream.println("Fetched "+ln.size()+" reads.");}
+			Read r=ln.get(0);
+			assert(ff.samOrBam() || (r.mate!=null)==cris.paired());
+		}
+
+		//As long as there is a nonempty read list...
+		while(ln!=null && ln.size()>0){
+			if(verbose){outstream.println("Fetched "+ln.size()+" reads.");}
+			for(Read r : ln){
+				final int tid=GiToTaxid.getID(r.id);
+				if(tid>=0 && r.length()>1000){
+					byte[] old=map.get(tid);
+					if(old==null || old.length<r.length()){map.put(tid, r.bases);}
+				}
+			}
+			cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
+
+			//Fetch a new list
+			ln=cris.nextList();
+		}
+
+		//Notify the input stream that the final list was used
+		if(ln!=null){
+			cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
+		}
+		errorState|=ReadWrite.closeStream(cris);
+		
+		return map;
+	}
+	
+	private static ConcurrentReadInputStream makeCris(FileFormat ff, PrintStream outstream){
+		if(verbose){outstream.println("makeCris");}
+		ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(-1, false, ff, null);
+		cris.start(); //Start the stream
+		if(verbose){outstream.println("Loading "+ff.name());}
+		boolean paired=cris.paired();
+		assert(!paired);
+//		if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
+		return cris;
+	}
+
+	public static boolean hasMap(){return r16SMap!=null || r18SMap!=null;}
+	public static int r16SCount(){return r16SMap==null ? 0 : r16SMap.size();}
+	public static int r18SCount(){return r18SMap==null ? 0 : r18SMap.size();}
+	
+	public static String r16SFile=null;
+	public static String r18SFile=null;
+	public static HashMap<Integer, byte[]> r16SMap=null;
+	public static HashMap<Integer, byte[]> r18SMap=null;
+	static boolean verbose=false;
+	static boolean errorState=false;
+	
+}