--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/icecream/IceCreamGrader.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,229 @@
+package icecream;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.ArrayList;
+
+import fileIO.ByteFile;
+import fileIO.ByteFile1;
+import fileIO.ByteFile2;
+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 stream.SamLine;
+import structures.ListNum;
+
+/**
+ * @author Brian Bushnell
+ * @date June 11, 2019
+ *
+ */
+public class IceCreamGrader {
+	
+	public static void main(String[] args){
+		//Start a timer immediately upon code entrance.
+		Timer t=new Timer();
+
+		//Create an instance of this class
+		IceCreamGrader x=new IceCreamGrader(args);
+
+		//Run the object
+		x.process(t);
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+	}
+	
+	public IceCreamGrader(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, getClass(), false);
+			args=pp.args;
+			outstream=pp.outstream;
+		}
+		
+		//Set shared static variables
+		Shared.capBuffers(4); //Only for singlethreaded programs
+		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
+		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
+		FASTQ.TEST_INTERLEAVED=FASTQ.FORCE_INTERLEAVED=false;
+		SamLine.SET_FROM_OK=true;
+		
+		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.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(parser.parse(arg, a, b)){
+				//do nothing
+			}
+			
+			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("=")){
+				parser.out1=arg;
+			}else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+				//				throw new RuntimeException("Unknown parameter "+args[i]);
+			}
+		}
+		
+		{//Process parser fields
+			Parser.processQuality();
+			
+			maxReads=parser.maxReads;
+			
+			overwrite=ReadStats.overwrite=parser.overwrite;
+			append=ReadStats.append=parser.append;
+			
+			in1=parser.in1;
+			
+			extin=parser.extin;
+		}
+		
+		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;
+		}
+
+		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
+	}
+	
+	void process(Timer t){
+		
+		final ConcurrentReadInputStream cris;
+		{
+			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null);
+			cris.start();
+			if(verbose){outstream.println("Started cris");}
+		}
+		
+		long readsProcessed=0, readsOut=0;
+		long basesProcessed=0, basesOut=0;
+		
+		{
+			
+			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(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
+				
+				final ArrayList<Read> listOut=new ArrayList<Read>(reads.size());
+				for(int idx=0; idx<reads.size(); idx++){
+					final Read r1=reads.get(idx);
+					
+					final int initialLength1=r1.length();
+					final boolean keep=process(r1);
+					if(keep){
+						listOut.add(r1);
+						readsOut++;
+						basesOut+=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|=ReadStats.writeAll();
+		
+		errorState|=ReadWrite.closeStreams(cris);
+		
+		t.stop();
+		outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
+//		outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false));
+		outstream.println();
+		outstream.println(Tools.numberPercent("Good Reads:", goodReads, goodReads*100.0/readsProcessed, 3, 8));
+		outstream.println(Tools.numberPercent("Good Bases:", goodBases, goodBases*100.0/basesProcessed, 3, 8));
+		outstream.println(Tools.numberPercent("Bad Reads:", badReads, badReads*100.0/readsProcessed, 3, 8));
+		outstream.println(Tools.numberPercent("Bad Bases:", badBases, badBases*100.0/basesProcessed, 3, 8));
+		
+		if(errorState){
+			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	private boolean process(Read r){
+		boolean iceCream=ReadBuilder.isIceCream(r.id);
+		if(iceCream){
+			badReads++;
+			badBases+=r.length();
+		}else{
+			goodReads++;
+			goodBases+=r.length();
+		}
+		return true;
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	private String in1=null;
+	
+	private String extin=null;
+	
+	/*--------------------------------------------------------------*/
+
+	private long maxReads=-1;
+
+	private long goodReads=0;
+	private long goodBases=0;
+	private long badReads=0;
+	private long badBases=0;
+	
+	/*--------------------------------------------------------------*/
+	
+	private final FileFormat ffin1;
+	
+	
+	/*--------------------------------------------------------------*/
+	
+	private PrintStream outstream=System.err;
+	public static boolean verbose=false;
+	public boolean errorState=false;
+	private boolean overwrite=false;
+	private boolean append=false;
+	
+}