--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/tax/AnalyzeAccession.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,446 @@
+package tax;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Locale;
+import java.util.Map.Entry;
+
+import fileIO.ByteFile;
+import fileIO.ByteFile1;
+import fileIO.ByteFile2;
+import fileIO.ByteStreamWriter;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import fileIO.TextFile;
+import shared.Parse;
+import shared.Parser;
+import shared.PreParser;
+import shared.Shared;
+import shared.Timer;
+import shared.Tools;
+import stream.ConcurrentGenericReadInputStream;
+import stream.FastaReadInputStream;
+import structures.ByteBuilder;
+import structures.ListNum;
+import structures.StringNum;
+import template.Accumulator;
+import template.ThreadWaiter;
+
+/**
+ * Counts patterns in Accessions.
+ * Handles hashing for Accession to TaxID lookups.
+ * @author Brian Bushnell
+ * @date May 9, 2018
+ *
+ */
+public class AnalyzeAccession implements Accumulator<AnalyzeAccession.ProcessThread> {
+	
+	public static void main(String[] args){
+		//Start a timer immediately upon code entrance.
+		Timer t=new Timer();
+		
+		//Create an instance of this class
+		AnalyzeAccession x=new AnalyzeAccession(args);
+		
+		//Run the object
+		x.process(t);
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+	}
+	
+	public AnalyzeAccession(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, getClass(), false);
+			args=pp.args;
+			outstream=pp.outstream;
+		}
+		
+		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
+		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
+		
+		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("in")){
+				if(b==null){in.clear();}
+				else{
+					String[] split2=b.split(",");
+					for(String s2 : split2){
+						in.add(s2);
+					}
+				}
+			}else if(a.equals("perfile")){
+				perFile=Parse.parseBoolean(b);
+			}else if(b==null && new File(arg).exists()){
+				in.add(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]);
+			}
+		}
+		
+		{//Process parser fields
+			overwrite=parser.overwrite;
+			append=parser.append;
+
+			out=parser.out1;
+		}
+		
+		assert(FastaReadInputStream.settingsOK());
+		
+		if(in==null){throw new RuntimeException("Error - at least one input file is required.");}
+		
+//		if(!ByteFile.FORCE_MODE_BF2){
+//			ByteFile.FORCE_MODE_BF2=false;
+//			ByteFile.FORCE_MODE_BF1=true;
+//		}
+
+		if(out!=null && out.equalsIgnoreCase("null")){out=null;}
+		
+		if(!Tools.testOutputFiles(overwrite, append, false, out)){
+			outstream.println((out==null)+", "+out);
+			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out+"\n");
+		}
+
+		ffout=FileFormat.testOutput(out, FileFormat.TXT, null, true, overwrite, append, false);
+		ffina=new FileFormat[in.size()];
+		for(int i=0; i<in.size(); i++){
+			ffina[i]=FileFormat.testInput(in.get(i), FileFormat.TXT, null, true, false);
+		}
+	}
+	
+	void process(Timer t){
+
+		if(perFile) {
+			process_perFile();
+		}else{
+			for(FileFormat ffin : ffina){
+				process_inner(ffin);
+			}
+		}
+		
+		if(ffout!=null){
+			ByteStreamWriter bsw=new ByteStreamWriter(ffout);
+			bsw.println("#Pattern\tCount\tCombos\tBits");
+			ArrayList<StringNum> list=new ArrayList<StringNum>();
+			list.addAll(countMap.values());
+			Collections.sort(list);
+			Collections.reverse(list);
+			for(StringNum sn : list){
+				double combos=1;
+				for(int i=0; i<sn.s.length(); i++){
+					char c=sn.s.charAt(i);
+					if(c=='D'){combos*=10;}
+					else if(c=='L'){combos*=26;}
+				}
+				bsw.print(sn.toString().getBytes());
+				bsw.println("\t"+(long)combos+"\t"+String.format(Locale.ROOT, "%.2f", Tools.log2(combos)));
+			}
+			bsw.start();
+			errorState|=bsw.poisonAndWait();
+		}
+		
+		t.stop();
+		
+		outstream.println(Tools.timeLinesBytesProcessed(t, linesProcessed, bytesProcessed, 8));
+		
+		outstream.println();
+		outstream.println("Valid Lines:       \t"+linesOut);
+		outstream.println("Invalid Lines:     \t"+(linesProcessed-linesOut));
+		
+		if(errorState){
+			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
+		}
+	}
+	
+	void process_inner(FileFormat ffin){
+		
+		ByteFile bf=ByteFile.makeByteFile(ffin);
+		
+		final int threads=Tools.min(8, Shared.threads());
+		ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
+		for(int i=0; i<threads; i++){alpt.add(new ProcessThread(bf));}
+		boolean success=ThreadWaiter.startAndWait(alpt, this);
+		errorState|=!success;
+	}
+	
+	
+	void process_perFile(){
+		ArrayList<ArrayList<ProcessThread>> perFileList=new ArrayList<ArrayList<ProcessThread>>(ffina.length);
+		for(FileFormat ffin : ffina) {
+			ByteFile bf=ByteFile.makeByteFile(ffin);
+
+			final int threads=Tools.min(16, Shared.threads());
+			ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
+			for(int i=0; i<threads; i++){alpt.add(new ProcessThread(bf));}
+			perFileList.add(alpt);
+			ThreadWaiter.startThreads(alpt);
+		}
+		for(ArrayList<ProcessThread> alpt : perFileList){
+			boolean success=ThreadWaiter.waitForThreads(alpt, this);
+			errorState|=!success;
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	static class ProcessThread extends Thread {
+		
+		ProcessThread(ByteFile bf_){
+			bf=bf_;
+		}
+		
+		@Override
+		public void run() {
+			final StringBuilder buffer=new StringBuilder(128);
+			for(ListNum<byte[]> lines=bf.nextList(); lines!=null; lines=bf.nextList()){
+				assert(lines.size()>0);
+				if(lines.id==0){
+					//This one is not really important; the header could be missing.
+					assert(Tools.startsWith(lines.get(0), "accession")) : bf.name()+"[0]: "+new String(lines.get(0));
+				}else{
+					assert(!Tools.startsWith(lines.get(0), "accession")) : bf.name()+"["+lines.id+"]: "+new String(lines.get(0));
+				}
+				for(byte[] line : lines){
+					if(line.length>0){
+						linesProcessedT++;
+						bytesProcessedT+=(line.length+1);
+						
+						boolean valid=lines.id>0 || !(Tools.startsWith(line, "accession")); //Skips test for most lines
+						
+						if(valid){
+							linesOutT++;
+							increment(line, buffer);
+						}
+					}
+				}
+			}
+		}
+		
+		void increment(byte[] line, StringBuilder buffer){
+			buffer.setLength(0);
+			for(int i=0; i<line.length; i++){
+				final byte b=line[i];
+				if(b==' ' || b=='\t' || b=='.' || b==':'){break;}
+				final char b2=(char)remap[b];
+				assert(b2!='?' || b=='+') : "unprocessed symbol in "+new String(line)+"\n"+"'"+(char)b+"'";
+				buffer.append(b2);
+			}
+			String key=buffer.toString();
+			StringNum value=countMapT.get(key);
+			if(value!=null){value.increment();}
+			else{countMapT.put(key, new StringNum(key, 1));}
+		}
+		
+		private HashMap<String, StringNum> countMapT=new HashMap<String, StringNum>();
+		private final ByteFile bf;
+		long linesProcessedT=0;
+		long linesOutT=0;
+		long bytesProcessedT=0;
+		
+	}
+	
+	/*--------------------------------------------------------------*/
+
+	@Override
+	public void accumulate(ProcessThread t) {
+		linesProcessed+=t.linesProcessedT;
+		linesOut+=t.linesOutT;
+		bytesProcessed+=t.bytesProcessedT;
+		for(Entry<String, StringNum> e : t.countMapT.entrySet()){
+			StringNum value=e.getValue();
+			final String key=e.getKey();
+			StringNum old=countMap.get(key);
+			if(old==null){countMap.put(key, value);}
+			else{old.add(value);}
+		}
+	}
+
+	@Override
+	public boolean success() {
+		return !errorState;
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	public static long combos(String s){
+		double combos=1;
+		for(int i=0; i<s.length(); i++){
+			char c=s.charAt(i);
+			if(c=='D'){combos*=10;}
+			else if(c=='L'){combos*=26;}
+		}
+		return (combos>=Long.MAX_VALUE ? Long.MAX_VALUE : (long)Math.ceil(combos));
+	}
+	
+	public static long combos(byte[] s){
+		double combos=1;
+		for(int i=0; i<s.length; i++){
+			byte c=s[i];
+			if(c=='D'){combos*=10;}
+			else if(c=='L'){combos*=26;}
+		}
+		return (combos>=Long.MAX_VALUE ? -1 : (long)Math.ceil(combos));
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	public static HashMap<String, Integer> loadCodeMap(String fname){
+		assert(codeMap==null);
+		TextFile tf=new TextFile(fname);
+		ArrayList<String> list=new ArrayList<String>();
+		for(String line=tf.nextLine(); line!=null; line=tf.nextLine()){
+			if(!line.startsWith("#")){
+				String[] split=line.split("\t");
+				list.add(split[0]);
+			}
+		}
+		HashMap<String, Integer> map=new HashMap<String, Integer>(list.size()*3);
+		codeBits=(int)Math.ceil(Tools.log2(list.size()));
+		final int patternBits=63-codeBits;
+		final long maxCombos=((1L<<(patternBits-1))-1);
+		for(int i=0; i<list.size(); i++){
+			String s=list.get(i);
+			longestPattern=Tools.max(longestPattern, s.length());
+			long combos=combos(s);
+			if(combos<0 || combos>=maxCombos){map.put(s, -1);}
+			else{map.put(s, i);}
+		}
+		codeMap=map;
+		return map;
+	}
+	
+	public static long digitize(String s){
+		String pattern=remap(s);
+		Integer code=codeMap.get(pattern);
+		if(code==null){return -2;}
+		if(code.intValue()<0){return -1;}
+		
+		long number=0;
+		for(int i=0; i<pattern.length(); i++){
+			char c=s.charAt(i);
+			char p=pattern.charAt(i);
+			if(p=='-' || p=='?'){
+				//do nothing
+			}else if(p=='D'){
+				number=(number*10)+(c-'0');
+			}else if(p=='L'){
+				number=(number*26)+(Tools.toUpperCase(c)-'A');
+			}else{
+				assert(false) : s;
+			}
+		}
+		number=(number<<codeBits)+code;
+		return number;
+	}
+	
+	public static long digitize(byte[] s){
+		String pattern=remap(s);
+		Integer code=codeMap.get(pattern);
+		if(code==null){return -2;}
+		if(code.intValue()<0){return -1;}
+		
+		long number=0;
+		for(int i=0; i<pattern.length(); i++){
+			byte c=s[i];
+			char p=pattern.charAt(i);
+			if(p=='-' || p=='?'){
+				//do nothing
+			}else if(p=='D'){
+				number=(number*10)+(c-'0');
+			}else if(p=='L'){
+				number=(number*26)+(Tools.toUpperCase(c)-'A');
+			}else{
+				assert(false) : new String(s);
+			}
+		}
+		number=(number<<codeBits)+code;
+		return number;
+	}
+	
+	public static String remap(String s){
+		if(s==null || s.length()<1){return "";}
+		ByteBuilder buffer=new ByteBuilder(s.length());
+		for(int i=0; i<s.length(); i++){
+			final char b=s.charAt(i);
+			if(b==' ' || b=='\t' || b=='.' || b==':'){break;}
+			buffer.append((char)remap[b]);
+		}
+		return buffer.toString();
+	}
+	
+	public static String remap(byte[] s){
+		ByteBuilder buffer=new ByteBuilder(s.length);
+		for(int i=0; i<s.length; i++){
+			final byte b=s[i];
+			if(b==' ' || b=='\t' || b=='.' || b==':'){break;}
+			buffer.append((char)remap[b]);
+		}
+		return buffer.toString();
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	private ArrayList<String> in=new ArrayList<String>();
+	private String out=null;
+	private boolean perFile=true;
+	
+	/*--------------------------------------------------------------*/
+
+	private HashMap<String, StringNum> countMap=new HashMap<String, StringNum>();
+	public static HashMap<String, Integer> codeMap;
+	private static int codeBits=-1;
+	private static int longestPattern=-1;
+	
+	private long linesProcessed=0;
+	private long linesOut=0;
+	private long bytesProcessed=0;
+	private long bytesOut=0;
+	
+	/*--------------------------------------------------------------*/
+	
+	private final FileFormat[] ffina;
+	private final FileFormat ffout;
+	
+	private static final byte[] remap=makeRemap();
+	
+	private static byte[] makeRemap(){
+		byte[] array=new byte[128];
+		Arrays.fill(array, (byte)'?');
+		for(int i='A'; i<='Z'; i++){array[i]='L';}
+		for(int i='a'; i<='z'; i++){array[i]='L';}
+		for(int i='0'; i<='9'; i++){array[i]='D';}
+		array['_']=array['-']='-';
+		return array;
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	private PrintStream outstream=System.err;
+	public static boolean verbose=false;
+	public boolean errorState=false;
+	private boolean overwrite=false;
+	private boolean append=false;
+	
+}