--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/shared/Parser.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,1493 @@
+package shared;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+
+import align2.QualityTools;
+import bloom.KCountArray;
+import bloom.KmerCountAbstract;
+import cardinality.CardinalityTracker;
+import cardinality.LogLog16;
+import cardinality.LogLog2;
+import dna.AminoAcid;
+import dna.Data;
+import fileIO.ByteFile;
+import fileIO.ByteFile1;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import fileIO.TextFile;
+import jgi.BBMerge;
+import jgi.CalcTrueQuality;
+import kmer.AbstractKmerTable;
+import sketch.SketchObject;
+import stream.ConcurrentDepot;
+import stream.ConcurrentReadInputStream;
+import stream.FASTQ;
+import stream.FastaReadInputStream;
+import stream.Read;
+import stream.ReadStreamByteWriter;
+import stream.ReadStreamWriter;
+import stream.SamLine;
+import stream.SamStreamer;
+import structures.EntropyTracker;
+import structures.IntList;
+import tax.TaxTree;
+import var2.CallVariants;
+
+/**
+ * @author Brian Bushnell
+ * @date Mar 21, 2014
+ *
+ */
+public class Parser {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public Parser(){}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------           Methods            ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public boolean parse(String arg, String a, String b){
+		if(isJavaFlag(arg)){return true;}
+
+		if(parseQuality(arg, a, b)){return true;}
+		if(parseZip(arg, a, b)){return true;}
+		if(parseSam(arg, a, b)){return true;}
+		if(parseFasta(arg, a, b)){return true;}
+		if(parseCommonStatic(arg, a, b)){return true;}
+		if(parseHist(arg, a, b)){return true;}
+		if(parseQualityAdjust(arg, a, b)){return true;}
+
+		if(parseFiles(arg, a, b)){return true;}
+		if(parseCommon(arg, a, b)){return true;}
+		if(parseTrim(arg, a, b)){return true;}
+		if(parseInterleaved(arg, a, b)){return true;}
+		if(parseMapping(arg, a, b)){return true;}
+		if(parseCardinality(arg, a, b)){return true;}
+		return false;
+	}
+
+	public boolean parseCommon(String arg, String a, String b){
+		if(a.equals("reads") || a.equals("maxreads")){
+			maxReads=Parse.parseKMG(b);
+		}else if(a.equals("samplerate")){
+			samplerate=Float.parseFloat(b);
+			assert(samplerate<=1f && samplerate>=0f) : "samplerate="+samplerate+"; should be between 0 and 1";
+		}else if(a.equals("sampleseed")){
+			sampleseed=Long.parseLong(b);
+		}else if(a.equals("append") || a.equals("app")){
+			append=ReadStats.append=Parse.parseBoolean(b);
+		}else if(a.equals("overwrite") || a.equals("ow")){
+			overwrite=Parse.parseBoolean(b);
+		}else if(a.equals("testsize")){
+			testsize=Parse.parseBoolean(b);
+		}else if(a.equals("breaklen") || a.equals("breaklength")){
+			breakLength=Integer.parseInt(b);
+		}else if(a.equals("recalibrate") || a.equals("recalibratequality") || a.equals("recal")){
+			recalibrateQuality=Parse.parseBoolean(b);
+		}else if(a.equals("silent")){
+			silent=Parse.parseBoolean(b);
+		}else{
+			return false;
+		}
+		return true;
+	}
+
+	public boolean parseCardinality(String arg, String a, String b){
+		if(a.equals("cardinality") || a.equals("loglog")){
+			if(b!=null && b.length()>0 && Tools.isDigit(b.charAt(0))){
+				try {
+					loglogk=Integer.parseInt(b);
+					loglog=loglogk>0;
+				} catch (NumberFormatException e) {
+					loglog=Parse.parseBoolean(b);
+				}
+			}else{
+				loglog=Parse.parseBoolean(b);
+			}
+		}else if(a.equals("cardinalityout") || a.equals("loglogout")){
+			if(b!=null && b.length()>0 && Tools.isDigit(b.charAt(0))){
+				try {
+					loglogk=Integer.parseInt(b);
+					loglogOut=loglogk>0;
+				} catch (NumberFormatException e) {
+					loglogOut=Parse.parseBoolean(b);
+				}
+			}else{
+				loglogOut=Parse.parseBoolean(b);
+			}
+		}else if(a.equals("buckets") || a.equals("loglogbuckets")){
+			loglogbuckets=Parse.parseIntKMG(b);
+			assert(loglogbuckets>0);
+			loglogbuckets=CardinalityTracker.powerOf2AtLeast(loglogbuckets);
+		}else if(a.equals("loglogbits")){
+			loglogbits=Integer.parseInt(b);
+		}else if(a.equals("loglogk") || a.equals("cardinalityk") || a.equals("kcardinality")){
+			loglogk=Integer.parseInt(b);
+			loglog=loglogk>0;
+		}else if(a.equals("loglogklist")){
+			String[] split2=b.split(",");
+			for(String k : split2){
+				loglogKlist.add(Integer.parseInt(k));
+			}
+		}else if(a.equals("loglogseed")){
+			loglogseed=Long.parseLong(b);
+		}else if(a.equals("loglogminprob")){
+			loglogMinprob=Float.parseFloat(b);
+		}else if(a.equals("loglogtype")){
+			loglogType=b;
+		}else if(a.equals("loglogmean")){
+			CardinalityTracker.USE_MEAN=true;
+			CardinalityTracker.USE_MEDIAN=CardinalityTracker.USE_MWA=CardinalityTracker.USE_HMEAN=CardinalityTracker.USE_GMEAN=false;
+		}else if(a.equals("loglogmedian")){
+			CardinalityTracker.USE_MEDIAN=true;
+			CardinalityTracker.USE_MEAN=CardinalityTracker.USE_MWA=CardinalityTracker.USE_HMEAN=CardinalityTracker.USE_GMEAN=false;
+		}else if(a.equals("loglogmwa")){
+			CardinalityTracker.USE_MWA=true;
+			CardinalityTracker.USE_MEDIAN=CardinalityTracker.USE_MEAN=CardinalityTracker.USE_HMEAN=CardinalityTracker.USE_GMEAN=false;
+		}else if(a.equals("logloghmean")){
+			CardinalityTracker.USE_HMEAN=true;
+			CardinalityTracker.USE_MEDIAN=CardinalityTracker.USE_MEAN=CardinalityTracker.USE_MWA=CardinalityTracker.USE_GMEAN=false;
+		}else if(a.equals("logloggmean")){
+			CardinalityTracker.USE_GMEAN=true;
+			CardinalityTracker.USE_MEDIAN=CardinalityTracker.USE_MEAN=CardinalityTracker.USE_HMEAN=CardinalityTracker.USE_MWA=false;
+		}else if(a.equals("loglogmantissa")){
+			LogLog2.setMantissaBits(Integer.parseInt(b));
+			LogLog16.setMantissaBits(Integer.parseInt(b));
+		}else if(a.equals("loglogcounts") || a.equals("loglogcount")){
+			CardinalityTracker.trackCounts=Parse.parseBoolean(b);
+		}else{
+			return false;
+		}
+		
+		return true;
+	}
+	
+	public boolean parseInterleaved(String arg, String a, String b){
+		if(a.equals("testinterleaved")){
+			FASTQ.TEST_INTERLEAVED=Parse.parseBoolean(b);
+			System.err.println("Set TEST_INTERLEAVED to "+FASTQ.TEST_INTERLEAVED);
+			setInterleaved=true;
+		}else if(a.equals("forceinterleaved")){
+			FASTQ.FORCE_INTERLEAVED=Parse.parseBoolean(b);
+			System.err.println("Set FORCE_INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
+			setInterleaved=true;
+		}else if(a.equals("interleaved") || a.equals("int")){
+			if("auto".equalsIgnoreCase(b)){FASTQ.FORCE_INTERLEAVED=!(FASTQ.TEST_INTERLEAVED=true);}
+			else{
+				FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=Parse.parseBoolean(b);
+				System.err.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
+				setInterleaved=true;
+			}
+		}else if(a.equals("overrideinterleaved")){
+			boolean x=Parse.parseBoolean(b);
+			ReadStreamByteWriter.ignorePairAssertions=x;
+			if(x){setInterleaved=true;}
+		}else{
+			return false;
+		}
+		return true;
+	}
+	
+	public boolean parseQTrim(String arg, String a, String b){
+		if(a.equals("qtrim1")){
+			if(b!=null && ("f".equalsIgnoreCase(b) || "false".equalsIgnoreCase(b))){qtrim1=false;}
+			else{
+				qtrim1=true;
+				qtrim2=false;
+			}
+			a="qtrim";
+		}else if(a.equals("qtrim2")){
+			if(b!=null && ("f".equalsIgnoreCase(b) || "false".equalsIgnoreCase(b))){qtrim2=false;}
+			else{
+				qtrim2=true;
+				qtrim1=false;
+			}
+			a="qtrim";
+		}else if(a.equals("trimq2")){
+			if(b!=null && ("f".equalsIgnoreCase(b) || "false".equalsIgnoreCase(b))){qtrim2=false;}
+			else{
+				qtrim2=true;
+				qtrim1=false;
+			}
+			a="trimq";
+		}
+		
+		if(a.equals("qtrim")/* || a.equals("trim")*/){
+			if(b==null || b.length()==0){qtrimRight=qtrimLeft=true;}
+			else if(b.equalsIgnoreCase("left") || b.equalsIgnoreCase("l")){qtrimLeft=true;qtrimRight=false;}
+			else if(b.equalsIgnoreCase("right") || b.equalsIgnoreCase("r")){qtrimLeft=false;qtrimRight=true;}
+			else if(b.equalsIgnoreCase("both") || b.equalsIgnoreCase("rl") || b.equalsIgnoreCase("lr")){qtrimLeft=qtrimRight=true;}
+			else if(b.equalsIgnoreCase("window") || b.equalsIgnoreCase("w") || b.startsWith("window,") || b.startsWith("w,")){
+				qtrimLeft=false;
+				qtrimRight=true;
+				TrimRead.windowMode=true;
+				TrimRead.optimalMode=false;
+				String[] split=b.split(",");
+				if(b.length()>1){
+					TrimRead.windowLength=Integer.parseInt(split[1]);
+				}
+			}else if(Tools.isDigit(b.charAt(0))){
+				parseTrimq(a, b);
+				qtrimRight=true;
+			}else{qtrimRight=qtrimLeft=Parse.parseBoolean(b);}
+		}else if(a.equals("optitrim") || a.equals("otf") || a.equals("otm")){
+			if(b!=null && (b.charAt(0)=='.' || Tools.isDigit(b.charAt(0)))){
+				TrimRead.optimalMode=true;
+				TrimRead.optimalBias=Float.parseFloat(b);
+				assert(TrimRead.optimalBias>=0 && TrimRead.optimalBias<1);
+			}else{
+				TrimRead.optimalMode=Parse.parseBoolean(b);
+			}
+		}else if(a.equals("trimgoodinterval")){
+			TrimRead.minGoodInterval=Integer.parseInt(b);
+		}else if(a.equals("trimright") || a.equals("qtrimright")){
+			qtrimRight=Parse.parseBoolean(b);
+		}else if(a.equals("trimleft") || a.equals("qtrimleft")){
+			qtrimLeft=Parse.parseBoolean(b);
+		}else if(a.equals("trimq") || a.equals("trimquality") || a.equals("trimq2")){
+			parseTrimq(a, b);
+		}else if(a.equals("trimclip")){
+			trimClip=Parse.parseBoolean(b);
+		}else if(a.equals("trimpolya")){
+			trimPolyA=parsePoly(b);
+		}
+		
+		else if(a.equals("trimpolyg")){
+			trimPolyGLeft=trimPolyGRight=parsePoly(b);
+		}else if(a.equals("trimpolygleft")){
+			trimPolyGLeft=parsePoly(b);
+		}else if(a.equals("trimpolygright")){
+			trimPolyGRight=parsePoly(b);
+		}else if(a.equals("filterpolyg")){
+			filterPolyG=parsePoly(b);
+		}
+		
+		else if(a.equals("trimpolyc")){
+			trimPolyCLeft=trimPolyCRight=parsePoly(b);
+		}else if(a.equals("trimpolycleft")){
+			trimPolyCLeft=parsePoly(b);
+		}else if(a.equals("trimpolycricht")){
+			trimPolyCRight=parsePoly(b);
+		}else if(a.equals("filterpolyc")){
+			filterPolyC=parsePoly(b);
+		}
+		
+		else{
+			return false;
+		}
+		return true;
+	}
+	
+	public static int parsePoly(String b){
+		int r=2;
+		if(b!=null){
+			if(Tools.isDigit(b.charAt(0))){
+				r=Integer.parseInt(b);
+			}else{
+				boolean x=Parse.parseBoolean(b);
+				r=x ? 2 : 0;
+			}
+		}
+		return r;
+	}
+	
+	public boolean parseTrim(String arg, String a, String b){
+		
+		if(parseQTrim(arg, a, b)){
+			//do nothing
+		}else if(a.equals("forcetrimmod") || a.equals("forcemrimmodulo") || a.equals("ftm")){
+			forceTrimModulo=Integer.parseInt(b);
+		}else if(a.equals("ftl") || a.equals("forcetrimleft")){
+			forceTrimLeft=Integer.parseInt(b);
+		}else if(a.equals("ftr") || a.equals("forcetrimright")){
+			forceTrimRight=Integer.parseInt(b);
+		}else if(a.equals("ftr2") || a.equals("forcetrimright2")){
+			forceTrimRight2=Integer.parseInt(b);
+		}else if(a.equals("trimbadsequence")){
+			trimBadSequence=Parse.parseBoolean(b);
+		}else if(a.equals("chastityfilter") || a.equals("cf")){
+			chastityFilter=Parse.parseBoolean(b);
+		}else if(a.equals("failnobarcode")){
+			failIfNoBarcode=Parse.parseBoolean(b);
+		}else if(a.equals("badbarcodes") || a.equals("barcodefilter")){
+			if(b!=null && (b.equalsIgnoreCase("crash") || b.equalsIgnoreCase("fail"))){
+				failBadBarcodes=true;
+				removeBadBarcodes=true;
+			}else{
+				removeBadBarcodes=Parse.parseBoolean(b);
+				failBadBarcodes=false;
+			}
+		}else if(a.equals("barcodes") || a.equals("barcode")){
+			if(b==null || b.length()<1){
+				barcodes=null;
+			}else{
+				barcodes=new HashSet<String>();
+				for(String s : b.split(",")){
+					Tools.addNames(s, barcodes, false);
+				}
+			}
+			if(barcodes!=null && barcodes.size()>0 && !failBadBarcodes && !removeBadBarcodes){
+				removeBadBarcodes=true;
+			}
+		}else if(a.equals("requirebothbad") || a.equals("rbb")){
+			requireBothBad=Parse.parseBoolean(b);
+		}else if(a.equals("removeifeitherbad") || a.equals("rieb")){
+			requireBothBad=!Parse.parseBoolean(b);
+		}else if(a.equals("ml") || a.equals("minlen") || a.equals("minlength")){
+			minReadLength=Parse.parseIntKMG(b);
+		}else if(a.equals("maxlength") || a.equals("maxreadlength") || a.equals("maxreadlen") || a.equals("maxlen")){
+			maxReadLength=Parse.parseIntKMG(b);
+		}else if(a.equals("mingc")){
+			minGC=Float.parseFloat(b);
+//			if(minGC>0){filterGC=true;}
+			assert(minGC>=0 && minGC<=1) : "mingc should be a decimal number between 0 and 1, inclusive.";
+		}else if(a.equals("maxgc")){
+			maxGC=Float.parseFloat(b);
+//			if(maxGC<1){filterGC=true;}
+			assert(minGC>=0 && minGC<=1) : "maxgc should be a decimal number between 0 and 1, inclusive.";
+		}else if(a.equals("usepairgc") || a.equals("pairgc")){
+			usePairGC=Parse.parseBoolean(b);
+			ReadStats.usePairGC=usePairGC;
+		}else if(a.equals("mlf") || a.equals("minlenfrac") || a.equals("minlenfraction") || a.equals("minlengthfraction")){
+			minLenFraction=Float.parseFloat(b);
+		}else if(a.equals("maxns")){
+			maxNs=Integer.parseInt(b);
+		}else if(a.equals("minconsecutivebases") || a.equals("mcb")){
+			minConsecutiveBases=Integer.parseInt(b);
+		}else if(a.equals("minavgquality") || a.equals("minaveragequality") || a.equals("maq")){
+			if(b.indexOf(',')>-1){
+				String[] split=b.split(",");
+				assert(split.length==2) : "maq should be length 1 or 2 (at most 1 comma).\nFormat: maq=quality,bases; e.g. maq=10 or maq=10,20";
+				minAvgQuality=Float.parseFloat(split[0]);
+				minAvgQualityBases=Integer.parseInt(split[1]);
+			}else{
+				minAvgQuality=Float.parseFloat(b);
+			}
+		}else if(a.equals("minavgqualitybases") || a.equals("maqb")){
+			minAvgQualityBases=Integer.parseInt(b);
+		}else if(a.equals("minbasequality") || a.equals("mbq")){
+			minBaseQuality=Byte.parseByte(b);
+		}else if(a.equals("averagequalitybyprobability") || a.equals("aqbp")){
+			Read.AVERAGE_QUALITY_BY_PROBABILITY=Parse.parseBoolean(b);
+		}else if(a.equals("mintl") || a.equals("mintrimlen") || a.equals("mintrimlength")){
+			minTrimLength=Integer.parseInt(b);
+		}else if(a.equals("untrim")){
+			untrim=Parse.parseBoolean(b);
+		}else if(a.equals("tossjunk")){
+			boolean x=Parse.parseBoolean(b);
+			tossJunk=x;
+			if(x){Read.JUNK_MODE=Read.FLAG_JUNK;}
+		}else{
+			return false;
+		}
+		return true;
+	}
+	
+	private void parseTrimq(String a, String b){
+		if(b.indexOf(',')>=0){
+			String[] split=b.split(",");
+			trimq2=new float[split.length];
+			for(int i=0; i<split.length; i++){
+				trimq2[i]=Float.parseFloat(split[i]);
+			}
+			trimq=trimq2.length<1 ? 0 : trimq2[0];
+		}else{
+			trimq=Float.parseFloat(b);
+			trimq2=null;
+		}
+//		assert(false) : Arrays.toString(trimq2);
+	}
+	
+	public boolean parseFiles(String arg, String a, String b){
+		if(a.equals("in") || a.equals("input") || a.equals("in1") || a.equals("input1")){
+			in1=b;
+		}else if(a.equals("in2") || a.equals("input2")){
+			in2=b;
+		}else if(a.equals("out") || a.equals("output") || a.equals("out1") || a.equals("output1")){
+			out1=b;
+			setOut=true;
+		}else if(a.equals("out2") || a.equals("output2")){
+			out2=b;
+			setOut=true;
+		}else if(a.equals("qfin") || a.equals("qfin1")){
+			qfin1=b;
+		}else if(a.equals("qfout") || a.equals("qfout1")){
+			qfout1=b;
+			setOut=true;
+		}else if(a.equals("qfin2")){
+			qfin2=b;
+		}else if(a.equals("qfout2")){
+			qfout2=b;
+			setOut=true;
+		}else if(a.equals("extin")){
+			extin=b;
+		}else if(a.equals("extout")){
+			extout=b;
+		}else if(a.equals("outsingle") || a.equals("outs")){
+			outsingle=b;
+			setOut=true;
+		}else{
+			return false;
+		}
+		return true;
+	}
+	
+	public boolean parseMapping(String arg, String a, String b){
+		if(a.equals("idfilter") || a.equals("identityfilter") || a.equals("minidfilter") || a.equals("minidentityfilter")){
+			minIdFilter=Float.parseFloat(b);
+			if(minIdFilter>1f){minIdFilter/=100;}
+			assert(minIdFilter<=1f) : "idfilter should be between 0 and 1.";
+		}else if(a.equals("maxidfilter") || a.equals("maxidentityfilter") || a.equals("maxid")){
+			maxIdFilter=Float.parseFloat(b);
+			if(maxIdFilter>1f){maxIdFilter/=100;}
+			assert(maxIdFilter<=1f) : "idfilter should be between 0 and 1.";
+		}else if(a.equals("subfilter")){
+			subfilter=Integer.parseInt(b);
+		}else if(a.equals("clipfilter")){
+			clipfilter=Integer.parseInt(b);
+		}else if(a.equals("nfilter")){
+			nfilter=Integer.parseInt(b);
+		}else if(a.equals("delfilter")){
+			delfilter=Integer.parseInt(b);
+		}else if(a.equals("insfilter")){
+			insfilter=Integer.parseInt(b);
+		}else if(a.equals("indelfilter")){
+			indelfilter=Integer.parseInt(b);
+		}else if(a.equals("dellenfilter")){
+			dellenfilter=Integer.parseInt(b);
+		}else if(a.equals("inslenfilter")){
+			inslenfilter=Integer.parseInt(b);
+		}else if(a.equals("editfilter")){
+			editfilter=Integer.parseInt(b);
+		}else if(a.equals("build") || a.equals("genome")){
+			build=Integer.parseInt(b);
+			Data.GENOME_BUILD=build;
+		}else{
+			return false;
+		}
+		return true;
+	}
+	
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Static Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	static String[] parseConfig(String[] args){
+		boolean found=false;
+		for(String s : args){
+			if(Tools.startsWithIgnoreCase(s, "config=")){
+				found=true;
+				break;
+			}
+		}
+		if(!found){return args;}
+		ArrayList<String> list=new ArrayList<String>();
+		for(int i=0; i<args.length; i++){
+			final String arg=(args[i]==null ? "null" : args[i]);
+			final String[] split=arg.split("=");
+			final String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+			if("null".equalsIgnoreCase(b)){b=null;}
+			
+			if(a.equals("config")){
+				assert(b!=null) : "Bad parameter: "+arg;
+				for(String bb : b.split(",")){
+					try{
+						TextFile tf=new TextFile(bb);
+						for(String line=tf.nextLine(); line!=null; line=tf.nextLine()){
+							String line2=line.trim();
+							if(line2.length()>0 && !line2.startsWith("#")){
+								list.add(line2);
+							}
+						}
+						tf.close();
+					}catch(Throwable t){
+						throw new RuntimeException("Could not process config file "+b+"\nCaused by:\n"+t.toString()+"\n");
+					}
+				}
+			}else if(arg!=null && !"null".equals(arg)){
+				list.add(arg);
+			}
+		}
+		return list.toArray(new String[list.size()]);
+	}
+	
+	public static boolean parseCommonStatic(String arg, String a, String b){
+		if(a.equals("null")){
+			//Do nothing
+		}else if(a.equals("monitor") || a.equals("killswitch")){
+			if(Parse.isNumber(b)){
+				String[] pair=b.split(",");
+				if(pair.length==1){
+					KillSwitch.launch(Double.parseDouble(pair[0]));
+				}else{
+					assert(pair.length==2) : "monitor takes one or two arguments, like this: monitor=600,0.002";
+					KillSwitch.launch(Double.parseDouble(pair[0]), Double.parseDouble(pair[1]));
+				}
+			}else if(Parse.parseBoolean(b)){
+				KillSwitch.launch();
+			}
+		}else if(a.equals("trd") || a.equals("trc") || a.equals("trimreaddescription") || a.equals("trimreaddescriptions")){
+			Shared.TRIM_READ_COMMENTS=Parse.parseBoolean(b);
+			if(!setTrimRname){Shared.TRIM_RNAME=Shared.TRIM_READ_COMMENTS;}
+		}else if(a.equals("trimrefdescription") || a.equals("trimrefdescriptions") || a.equals("trimrname")){
+			Shared.TRIM_RNAME=Parse.parseBoolean(b);
+			setTrimRname=true;
+		}else if(a.equals("tuc") || a.equals("touppercase")){
+			Read.TO_UPPER_CASE=Parse.parseBoolean(b);
+		}else if(a.equals("lctn") || a.equals("lowercaseton")){
+			Read.LOWER_CASE_TO_N=Parse.parseBoolean(b);
+		}else if(a.equals("changequality") || a.equals("cq")){
+			Read.CHANGE_QUALITY=Parse.parseBoolean(b);
+			BBMerge.changeQuality=Read.CHANGE_QUALITY;
+		}else if(a.equals("tossbrokenreads") || a.equals("tbr")){
+			boolean x=Parse.parseBoolean(b);
+			Read.TOSS_BROKEN_QUALITY=x;
+			ConcurrentReadInputStream.REMOVE_DISCARDED_READS=x;
+		}else if(a.equals("nullifybrokenquality") || a.equals("nbq")){
+			boolean x=Parse.parseBoolean(b);
+			Read.NULLIFY_BROKEN_QUALITY=x;
+		}else if(a.equals("dotdashxton")){
+			boolean x=Parse.parseBoolean(b);
+			Read.DOT_DASH_X_TO_N=x;
+		}else if(a.equals("junk")){
+			if("ignore".equalsIgnoreCase(b)){Read.JUNK_MODE=Read.IGNORE_JUNK;}
+			else if("crash".equalsIgnoreCase(b) || "fail".equalsIgnoreCase(b)){Read.JUNK_MODE=Read.CRASH_JUNK;}
+			else if("fix".equalsIgnoreCase(b)){Read.JUNK_MODE=Read.FIX_JUNK;}
+			else if("flag".equalsIgnoreCase(b) || "discard".equalsIgnoreCase(b)){Read.JUNK_MODE=Read.FLAG_JUNK;}
+			else if("iupacton".equalsIgnoreCase(b)){Read.JUNK_MODE=Read.FIX_JUNK_AND_IUPAC;}
+			else{assert(false) : "Bad junk mode: "+arg;}
+		}else if(a.equals("undefinedton") || a.equals("iupacton") || a.equals("itn")){
+			Read.IUPAC_TO_N=Parse.parseBoolean(b);
+		}else if(a.equals("ignorejunk")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){Read.JUNK_MODE=Read.IGNORE_JUNK;}
+			else if(Read.JUNK_MODE==Read.IGNORE_JUNK){Read.JUNK_MODE=Read.CRASH_JUNK;}
+		}else if(a.equals("flagjunk")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){Read.JUNK_MODE=Read.FLAG_JUNK;}
+			else if(Read.JUNK_MODE==Read.FLAG_JUNK){Read.JUNK_MODE=Read.CRASH_JUNK;}
+		}else if(a.equals("fixjunk")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){Read.JUNK_MODE=Read.FIX_JUNK;}
+			else if(Read.JUNK_MODE==Read.FIX_JUNK){Read.JUNK_MODE=Read.CRASH_JUNK;}
+		}else if(a.equals("crashjunk") || a.equals("failjunk")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){Read.JUNK_MODE=Read.CRASH_JUNK;}
+			else if(Read.JUNK_MODE==Read.CRASH_JUNK){Read.JUNK_MODE=Read.IGNORE_JUNK;}
+		}else if(a.equals("skipvalidation")){
+			Read.SKIP_SLOW_VALIDATION=Parse.parseBoolean(b);
+		}else if(a.equals("validate")){
+			Read.SKIP_SLOW_VALIDATION=!Parse.parseBoolean(b);
+		}else if(a.equals("validatebranchless")){
+//			Read.VALIDATE_BRANCHLESS=Parse.parseBoolean(b);
+		}else if(a.equals("bf1")){
+			ByteFile.FORCE_MODE_BF1=Parse.parseBoolean(b);
+			ByteFile.FORCE_MODE_BF2=!ByteFile.FORCE_MODE_BF1;
+		}else if(a.equals("bf1bufferlen")){
+			ByteFile1.bufferlen=(int)Parse.parseKMGBinary(b);
+		}else if(a.equals("utot")){
+			Read.U_TO_T=Parse.parseBoolean(b);
+		}else if(a.equals("bf2")){
+			ByteFile.FORCE_MODE_BF2=Parse.parseBoolean(b);
+			ByteFile.FORCE_MODE_BF1=!ByteFile.FORCE_MODE_BF2;
+		}else if(a.equals("bf3")){
+			ByteFile.FORCE_MODE_BF3=Parse.parseBoolean(b);
+			if(ByteFile.FORCE_MODE_BF3){
+				ByteFile.FORCE_MODE_BF1=true;
+				ByteFile.FORCE_MODE_BF2=false;
+			}
+		}else if(a.equals("usejni") || a.equals("jni")){
+			Shared.USE_JNI=Parse.parseBoolean(b);
+		}else if(a.equals("usempi") || a.equals("mpi")){
+			if(b!=null && Tools.isDigit(b.charAt(0))){
+				Shared.MPI_NUM_RANKS=Integer.parseInt(b);
+				Shared.USE_MPI=Shared.MPI_NUM_RANKS>0;
+			}else{
+				Shared.USE_MPI=Parse.parseBoolean(b);
+			}
+		}else if(a.equals("crismpi")){
+			Shared.USE_CRISMPI=Parse.parseBoolean(b);
+		}else if(a.equals("mpikeepall")){
+			Shared.MPI_KEEP_ALL=Parse.parseBoolean(b);
+		}else if(a.equals("readbufferlength") || a.equals("readbufferlen")){
+			Shared.setBufferLen((int)Parse.parseKMG(b));
+		}else if(a.equals("readbufferdata")){
+			Shared.setBufferData(Parse.parseKMG(b));
+		}else if(a.equals("readbuffers")){
+			Shared.setBuffers(Integer.parseInt(b));
+		}else if(a.equals("rbm") || a.equals("renamebymapping")){
+			FASTQ.TAG_CUSTOM=Parse.parseBoolean(b);
+		}else if(a.equals("don") || a.equals("deleteoldname")){
+			FASTQ.DELETE_OLD_NAME=Parse.parseBoolean(b);
+		}else if(a.equals("assertcigar")){
+			ReadStreamWriter.ASSERT_CIGAR=Parse.parseBoolean(b);
+		}else if(a.equals("verbosesamline")){
+			SamLine.verbose=Parse.parseBoolean(b);
+		}else if(a.equals("parsecustom") || a.equals("fastqparsecustom")){
+			FASTQ.PARSE_CUSTOM=Parse.parseBoolean(b);
+			System.err.println("Set FASTQ.PARSE_CUSTOM to "+FASTQ.PARSE_CUSTOM);
+		}else if(a.equals("fairqueues")){
+			ConcurrentDepot.fair=Parse.parseBoolean(b);
+		}else if(a.equals("fixheader") || a.equals("fixheaders")){
+			Read.FIX_HEADER=Parse.parseBoolean(b);
+		}else if(a.equals("allownullheader") || a.equals("allownullheaders")){
+			Read.ALLOW_NULL_HEADER=Parse.parseBoolean(b);
+		}else if(a.equals("aminoin") || a.equals("amino")){
+			//TODO: ensure changes to this do not conflict with TranslateSixFrames "aain" flag.
+			Shared.AMINO_IN=SketchObject.amino=Parse.parseBoolean(b);
+		}else if(a.equals("amino8")){
+			SketchObject.amino8=Parse.parseBoolean(b);
+			if(SketchObject.amino8){
+				Shared.AMINO_IN=SketchObject.amino=true;
+				AminoAcid.AMINO_SHIFT=3;
+			}
+		}else if(a.equals("maxcalledquality")){
+			int x=Tools.mid(1, Integer.parseInt(b), 93);
+			Read.setMaxCalledQuality((byte)x);
+		}else if(a.equals("mincalledquality")){
+			int x=Tools.mid(0, Integer.parseInt(b), 93);
+			Read.setMinCalledQuality((byte)x);
+		}else if(a.equals("t") || a.equals("threads")){
+			Shared.setThreads(b);
+			if(!silent){System.err.println("Set threads to "+Shared.threads());}
+		}else if(a.equals("recalpairnum") || a.equals("recalibratepairnum")){
+			CalcTrueQuality.USE_PAIRNUM=Parse.parseBoolean(b);
+		}else if(a.equals("taxpath")){
+			if("auto".equalsIgnoreCase(b)){
+				TaxTree.TAX_PATH=TaxTree.defaultTaxPath();
+			}else{
+				TaxTree.TAX_PATH=b.replaceAll("\\\\", "/");
+			}
+		}else if(a.equals("parallelsort")){
+			boolean x=Parse.parseBoolean(b);
+			Shared.setParallelSort(x);
+		}else if(a.equals("gcbeforemem")){
+			Shared.GC_BEFORE_PRINT_MEMORY=Parse.parseBoolean(b);
+		}else if(a.equals("warnifnosequence")){
+			FastaReadInputStream.WARN_IF_NO_SEQUENCE=Parse.parseBoolean(b);
+		}else if(a.equals("warnfirsttimeonly")){
+			FastaReadInputStream.WARN_FIRST_TIME_ONLY=Parse.parseBoolean(b);
+		}else if(a.equals("silva")){
+			TaxTree.SILVA_MODE=Parse.parseBoolean(b);
+		}else if(a.equals("unite")){
+			TaxTree.UNITE_MODE=Parse.parseBoolean(b);
+		}else if(a.equals("parallelsort") || a.equals("paralellsort")){
+			Shared.parallelSort=Parse.parseBoolean(b);
+		}else if(a.equals("imghq")){
+			TaxTree.IMG_HQ=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equals("callins") ||  a.equals("callinss")){
+			var2.Var.CALL_INS=Parse.parseBoolean(b);
+		}else if(a.equals("calldel") || a.equals("calldels")){
+			var2.Var.CALL_DEL=Parse.parseBoolean(b);
+		}else if(a.equals("callsub") || a.equals("callsubs") || a.equals("callsnp") || a.equals("callsnps")){
+			var2.Var.CALL_SUB=Parse.parseBoolean(b);
+		}else if(a.equals("callindel") || a.equals("callindels")){
+			var2.Var.CALL_INS=var2.Var.CALL_DEL=Parse.parseBoolean(b);
+		}else if(a.equals("calljunct") || a.equals("calljunction") || a.equals("calljunctions")){
+			var2.Var.CALL_JUNCTION=Parse.parseBoolean(b);
+		}else if(a.equals("callnocall") || a.equals("callnocalls")){
+			var2.Var.CALL_NOCALL=Parse.parseBoolean(b);
+		}else if(a.equals("kmg") || a.equals("outputkmg")){
+			Shared.OUTPUT_KMG=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equals("tmpdir")){
+			Shared.setTmpdir(b);
+		}
+		
+		else if(a.equals("comment")){
+			Shared.comment=b;
+		}
+		
+		else if(a.equals("fixextensions") || a.equals("fixextension") || a.equals("tryallextensions")){
+			Shared.FIX_EXTENSIONS=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equals("2passresize") || a.equals("twopassresize")){
+			AbstractKmerTable.TWO_PASS_RESIZE=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("forceJavaParseDouble")){
+			Tools.FORCE_JAVA_PARSE_DOUBLE=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("awsServers") || a.equalsIgnoreCase("aws")){
+			Shared.awsServers=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("nerscServers") || a.equalsIgnoreCase("nersc")){
+			Shared.awsServers=!Parse.parseBoolean(b);
+		}
+		
+		else if(a.equals("entropyk") || a.equals("ek")){
+			EntropyTracker.defaultK=Integer.parseInt(b);
+			EntropyTracker.setDefaultK=true;
+		}else if(a.equals("entropywindow") || a.equals("ew")){
+			EntropyTracker.defaultWindowBases=Integer.parseInt(b);
+			EntropyTracker.setDefaultWindow=true;
+		}else if(a.equalsIgnoreCase("protFull")){
+			TaxTree.protFull=true;
+		}
+		
+		else if(a.equalsIgnoreCase("lockedincrement") || a.equalsIgnoreCase("symmetricwrite")
+				|| a.equalsIgnoreCase("symmetric") || a.equalsIgnoreCase("sw")){
+			if("auto".equalsIgnoreCase(b)){
+				KCountArray.LOCKED_INCREMENT=true;
+				KCountArray.SET_LOCKED_INCREMENT=false;
+			}else{
+				KCountArray.LOCKED_INCREMENT=Parse.parseBoolean(b);
+				KCountArray.SET_LOCKED_INCREMENT=true;
+			}
+		}
+		
+		else if(a.equalsIgnoreCase("buffer") || a.equalsIgnoreCase("buffered")){
+			if(b!=null && Character.isDigit(b.charAt(0))){
+				int x=Parse.parseIntKMG(b);
+				KmerCountAbstract.BUFFERED=x>1;
+				if(x>1){KmerCountAbstract.BUFFERLEN=x;}
+			}else{
+				KmerCountAbstract.BUFFERED=Parse.parseBoolean(b);
+			}
+		}
+//		else if(a.equalsIgnoreCase("sortserial")){
+//			KmerCountAbstract.SORT_SERIAL=Parse.parseBoolean(b);
+//		}
+		
+		else{
+			return false;
+		}
+		return true;
+	}
+	
+	public static boolean parseQuality(String arg, String a, String b){
+		parsedQuality=true; //For internal verification that this function was indeed called.
+		if(a.equals("ignorebadquality") || a.equals("ibq")){
+			FASTQ.IGNORE_BAD_QUALITY=Parse.parseBoolean(b);
+			if(FASTQ.IGNORE_BAD_QUALITY){Read.CHANGE_QUALITY=false;}
+		}else if(a.equals("ascii") || a.equals("asciioffset") || a.equals("quality") || a.equals("qual")){
+			byte x;
+			if(b.equalsIgnoreCase("sanger")){x=33;}
+			else if(b.equalsIgnoreCase("illumina")){x=64;}
+			else if(b.equalsIgnoreCase("auto")){x=-1;FASTQ.DETECT_QUALITY=FASTQ.DETECT_QUALITY_OUT=true;}
+			else{x=(byte)Integer.parseInt(b);}
+			qin=qout=x;
+			FASTQ.SET_QIN=x>-1;
+		}else if(a.equals("asciiin") || a.equals("qualityin") || a.equals("qualin") || a.equals("qin")){
+			byte x;
+			if(b.equalsIgnoreCase("sanger")){x=33;}
+			else if(b.equalsIgnoreCase("illumina")){x=64;}
+			else if(b.equalsIgnoreCase("auto")){x=-1;FASTQ.DETECT_QUALITY=true;}
+			else{x=(byte)Integer.parseInt(b);}
+			qin=x;
+			FASTQ.SET_QIN=x>-1;
+		}else if(a.equals("asciiout") || a.equals("qualityout") || a.equals("qualout") || a.equals("qout")){
+			byte x;
+			if(b.equalsIgnoreCase("sanger")){x=33;}
+			else if(b.equalsIgnoreCase("illumina")){x=64;}
+			else if(b.equalsIgnoreCase("auto")){x=-1;FASTQ.DETECT_QUALITY_OUT=true;}
+			else{x=(byte)Integer.parseInt(b);}
+			qout=x;
+		}else if(a.equals("fakequality") || a.equals("qfake")){
+			Shared.FAKE_QUAL=Byte.parseByte(b);
+		}else if(a.equals("fakefastaqual") || a.equals("fakefastaquality") || a.equals("ffq")){
+			if(b==null || b.length()<1){b="f";}
+			if(Character.isLetter(b.charAt(0))){
+				FastaReadInputStream.FAKE_QUALITY=Parse.parseBoolean(b);
+			}else{
+				int x=Integer.parseInt(b);
+				if(x<1){
+					FastaReadInputStream.FAKE_QUALITY=false;
+				}else{
+					FastaReadInputStream.FAKE_QUALITY=true;
+					Shared.FAKE_QUAL=(byte)Tools.min(x, 50);
+				}
+			}
+		}else if(a.equals("qauto")){
+			FASTQ.DETECT_QUALITY=FASTQ.DETECT_QUALITY_OUT=true;
+		}else{
+			return false;
+		}
+		return true;
+	}
+	
+	private static boolean qhistsNull(){
+		return ReadStats.BQUAL_HIST_FILE==null && ReadStats.QUAL_HIST_FILE!=null && ReadStats.AVG_QUAL_HIST_FILE!=null && ReadStats.BQUAL_HIST_OVERALL_FILE!=null
+				&& ReadStats.QUAL_COUNT_HIST_FILE==null;
+	}
+	
+	public static boolean parseHist(String arg, String a, String b){
+		if(a.equals("qualityhistogram") || a.equals("qualityhist") || a.equals("qhist")){
+			ReadStats.QUAL_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_QUALITY_STATS=!qhistsNull();
+			if(ReadStats.COLLECT_QUALITY_STATS){System.err.println("Set quality histogram output to "+ReadStats.QUAL_HIST_FILE);}
+		}else if(a.equals("basequalityhistogram") || a.equals("basequalityhist") || a.equals("bqhist")){
+			ReadStats.BQUAL_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_QUALITY_STATS=!qhistsNull();
+			if(ReadStats.BQUAL_HIST_FILE!=null){System.err.println("Set bquality histogram output to "+ReadStats.BQUAL_HIST_FILE);}
+		}else if(a.equals("qualitycounthistogram") || a.equals("qualitycounthist") || a.equals("qchist") || a.equals("qdhist") || a.equals("qfhist")){
+			ReadStats.QUAL_COUNT_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_QUALITY_STATS=!qhistsNull();
+			if(ReadStats.QUAL_COUNT_HIST_FILE!=null){System.err.println("Set qcount histogram output to "+ReadStats.QUAL_COUNT_HIST_FILE);}
+		}else if(a.equals("averagequalityhistogram") || a.equals("aqhist")){
+			ReadStats.AVG_QUAL_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_QUALITY_STATS=!qhistsNull();
+			if(ReadStats.COLLECT_QUALITY_STATS){System.err.println("Set average quality histogram output to "+ReadStats.AVG_QUAL_HIST_FILE);}
+		}else if(a.equals("overallbasequalityhistogram") || a.equals("overallbasequalityhist") || a.equals("obqhist")){
+			ReadStats.BQUAL_HIST_OVERALL_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_QUALITY_STATS=(ReadStats.BQUAL_HIST_FILE!=null || ReadStats.QUAL_HIST_FILE!=null || ReadStats.AVG_QUAL_HIST_FILE!=null || ReadStats.BQUAL_HIST_OVERALL_FILE!=null);
+			if(ReadStats.COLLECT_QUALITY_STATS){System.err.println("Set quality histogram output to "+ReadStats.QUAL_HIST_FILE);}
+		}else if(a.equals("matchhistogram") || a.equals("matchhist") || a.equals("mhist")){
+			ReadStats.MATCH_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_MATCH_STATS=(ReadStats.MATCH_HIST_FILE!=null);
+			if(ReadStats.COLLECT_MATCH_STATS){System.err.println("Set match histogram output to "+ReadStats.MATCH_HIST_FILE);}
+		}else if(a.equals("inserthistogram") || a.equals("inserthist") || a.equals("ihist")){
+			ReadStats.INSERT_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_INSERT_STATS=(ReadStats.INSERT_HIST_FILE!=null);
+			if(ReadStats.COLLECT_INSERT_STATS){System.err.println("Set insert size histogram output to "+ReadStats.INSERT_HIST_FILE);}
+		}else if(a.equals("basehistogram") || a.equals("basehist") || a.equals("bhist")){
+			ReadStats.BASE_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_BASE_STATS=(ReadStats.BASE_HIST_FILE!=null);
+			if(ReadStats.COLLECT_BASE_STATS){System.err.println("Set base content histogram output to "+ReadStats.BASE_HIST_FILE);}
+		}else if(a.equals("qualityaccuracyhistogram") || a.equals("qahist")){
+			ReadStats.QUAL_ACCURACY_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_QUALITY_ACCURACY=(ReadStats.QUAL_ACCURACY_FILE!=null);
+			if(ReadStats.COLLECT_QUALITY_ACCURACY){System.err.println("Set quality accuracy histogram output to "+ReadStats.QUAL_ACCURACY_FILE);}
+		}else if(a.equals("indelhistogram") || a.equals("indelhist")){
+			ReadStats.INDEL_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_INDEL_STATS=(ReadStats.INDEL_HIST_FILE!=null);
+			if(ReadStats.COLLECT_INDEL_STATS){System.err.println("Set indel histogram output to "+ReadStats.INDEL_HIST_FILE);}
+		}else if(a.equals("errorhistogram") || a.equals("ehist")){
+			ReadStats.ERROR_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_ERROR_STATS=(ReadStats.ERROR_HIST_FILE!=null);
+			if(ReadStats.COLLECT_ERROR_STATS){System.err.println("Set error histogram output to "+ReadStats.ERROR_HIST_FILE);}
+		}else if(a.equals("lengthhistogram") || a.equals("lhist")){
+			ReadStats.LENGTH_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_LENGTH_STATS=(ReadStats.LENGTH_HIST_FILE!=null);
+			if(ReadStats.COLLECT_LENGTH_STATS){System.err.println("Set length histogram output to "+ReadStats.LENGTH_HIST_FILE);}
+		}else if(a.equals("gchistogram") || a.equals("gchist")){
+			ReadStats.GC_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_GC_STATS=(ReadStats.GC_HIST_FILE!=null);
+			if(ReadStats.COLLECT_GC_STATS){System.err.println("Set GC histogram output to "+ReadStats.GC_HIST_FILE);}
+		}else if(a.equals("gcbins") || a.equals("gchistbins")){
+			if("auto".equalsIgnoreCase(b)){
+				ReadStats.GC_BINS=4000;
+				ReadStats.GC_BINS_AUTO=true;
+			}else{
+				ReadStats.GC_BINS=Integer.parseInt(b);
+				ReadStats.GC_BINS_AUTO=false;
+			}
+		}else if(a.equals("gcchart") || a.equals("gcplot")){
+			ReadStats.GC_PLOT_X=Parse.parseBoolean(b);
+		}else if(a.equals("entropyhistogram") || a.equals("entropyhist") || a.equals("enhist") || a.equals("enthist")){
+			ReadStats.ENTROPY_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_ENTROPY_STATS=(ReadStats.ENTROPY_HIST_FILE!=null);
+			if(ReadStats.COLLECT_ENTROPY_STATS){System.err.println("Set entropy histogram output to "+ReadStats.ENTROPY_HIST_FILE);}
+		}else if(a.equals("entropybins") || a.equals("entropyhistbins") || a.equals("entbins") || a.equals("enthistbins")){
+			if("auto".equalsIgnoreCase(b)){
+				ReadStats.ENTROPY_BINS=1000;
+//				ReadStats.ENTROPY_BINS_AUTO=true;
+			}else{
+				ReadStats.ENTROPY_BINS=Integer.parseInt(b);
+//				ReadStats.ENTROPY_BINS_AUTO=false;
+			}
+		}else if(a.equals("entropyns") || a.equals("entropyhistns")){
+			ReadStats.allowEntropyNs=Parse.parseBoolean(b);
+		}else if(a.equals("timehistogram") || a.equals("thist")){
+			ReadStats.TIME_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_TIME_STATS=(ReadStats.TIME_HIST_FILE!=null);
+			if(ReadStats.COLLECT_IDENTITY_STATS){System.err.println("Set identity histogram output to "+ReadStats.IDENTITY_HIST_FILE);}
+		}else if(a.equals("identityhistogram") || a.equals("idhist")){
+			ReadStats.IDENTITY_HIST_FILE=(b==null || b.equalsIgnoreCase("null") || b.equalsIgnoreCase("none")) ? null : b;
+			ReadStats.COLLECT_IDENTITY_STATS=(ReadStats.IDENTITY_HIST_FILE!=null);
+			if(ReadStats.COLLECT_IDENTITY_STATS){System.err.println("Set identity histogram output to "+ReadStats.IDENTITY_HIST_FILE);}
+		}else if(a.equals("idhistlen") || a.equals("idhistlength") || a.equals("idhistbins") || a.equals("idbins")){
+			if("auto".equalsIgnoreCase(b)){
+				ReadStats.ID_BINS=750;
+				ReadStats.ID_BINS_AUTO=true;
+			}else{
+				ReadStats.ID_BINS=Integer.parseInt(b);
+				ReadStats.ID_BINS_AUTO=false;
+			}
+		}
+		
+		else if(a.equals("maxhistlen")){
+			ReadStats.MAXLEN=ReadStats.MAXINSERTLEN=ReadStats.MAXLENGTHLEN=Parse.parseIntKMG(b);
+		}
+		
+		else if(a.equals("fixindels") || a.equals("ignorevcfindels")){
+			CallVariants.fixIndels=Parse.parseBoolean(b);
+		}
+		
+		else{
+			return false;
+		}
+		return true;
+	}
+
+	public static boolean parseZip(String arg, String a, String b){
+		if(a.equals("ziplevel") || a.equals("zl")){
+			int x=Integer.parseInt(b);
+			if(x>=0){
+				ReadWrite.ZIPLEVEL=Tools.min(x, 11);
+			}
+		}else if(a.equals("bziplevel") || a.equals("bzl")){
+			int x=Integer.parseInt(b);
+			if(x>=0){
+				ReadWrite.BZIPLEVEL=Tools.min(x, 9);
+			}
+		}else if(a.equals("allowziplevelchange")){
+			ReadWrite.ALLOW_ZIPLEVEL_CHANGE=Parse.parseBoolean(b);
+		}else if(a.equals("usegzip") || a.equals("gzip")){
+			ReadWrite.USE_GZIP=Parse.parseBoolean(b);
+		}else if(a.equals("usebgzip") || a.equals("bgzip")){
+			
+			if(b!=null && Tools.isDigit(b.charAt(0))){
+				int zt=Integer.parseInt(b);
+				if(zt<1){ReadWrite.USE_BGZIP=false;}
+				else{
+					ReadWrite.USE_BGZIP=true;
+					ReadWrite.MAX_ZIP_THREADS=zt;
+				}
+			}else{ReadWrite.USE_BGZIP=Parse.parseBoolean(b);}
+			if(ReadWrite.USE_BGZIP){ReadWrite.PREFER_BGZIP=true;}
+		}else if(a.equals("forcepigz")){
+			ReadWrite.FORCE_PIGZ=Parse.parseBoolean(b);
+			if(ReadWrite.FORCE_PIGZ){ReadWrite.USE_PIGZ=true;}
+		}else if(a.equals("forcebgzip")){
+			ReadWrite.FORCE_BGZIP=Parse.parseBoolean(b);
+			if(ReadWrite.FORCE_BGZIP){ReadWrite.USE_BGZIP=true;}
+		}else if(a.equals("preferbgzip")){
+			ReadWrite.PREFER_BGZIP=Parse.parseBoolean(b);
+		}else if(a.equals("zipthreads")){
+			ReadWrite.MAX_ZIP_THREADS=Integer.parseInt(b);
+		}else if(a.equals("usepigz") || a.equals("pigz")){
+			if(b!=null && Tools.isDigit(b.charAt(0))){
+				int zt=Integer.parseInt(b);
+				if(zt<1){ReadWrite.USE_PIGZ=false;}
+				else{
+					ReadWrite.USE_PIGZ=true;
+					ReadWrite.MAX_ZIP_THREADS=zt;
+				}
+			}else{ReadWrite.USE_PIGZ=Parse.parseBoolean(b);}
+		}else if(a.equals("zipthreaddivisor") || a.equals("ztd")){
+			ReadWrite.setZipThreadMult(1/Float.parseFloat(b));
+		}else if(a.equals("blocksize")){
+			int x=Integer.parseInt(b);
+			ReadWrite.PIGZ_BLOCKSIZE=Tools.mid(32, x, 1024);
+		}else if(a.equals("pigziterations") || a.equals("pigziters")){
+			int x=Integer.parseInt(b);
+			ReadWrite.PIGZ_ITERATIONS=Tools.mid(32, x, 1024);
+		}else if(a.equals("usegunzip") || a.equals("gunzip") || a.equals("ungzip")){
+			ReadWrite.USE_GUNZIP=Parse.parseBoolean(b);
+		}else if(a.equals("useunpigz") || a.equals("unpigz")){
+			ReadWrite.USE_UNPIGZ=Parse.parseBoolean(b);
+		}else if(a.equals("useunbgzip") || a.equals("unbgzip")){
+			ReadWrite.USE_UNBGZIP=ReadWrite.PREFER_UNBGZIP=Parse.parseBoolean(b);
+		}else if(a.equals("preferunbgzip")){
+			ReadWrite.PREFER_UNBGZIP=Parse.parseBoolean(b);
+		}else if(a.equals("usebzip2") || a.equals("bzip2")){
+			ReadWrite.USE_BZIP2=Parse.parseBoolean(b);
+		}else if(a.equals("usepbzip2") || a.equals("pbzip2")){
+			ReadWrite.USE_PBZIP2=Parse.parseBoolean(b);
+		}else if(a.equals("uselbzip2") || a.equals("lbzip2")){
+			ReadWrite.USE_LBZIP2=Parse.parseBoolean(b);
+		}else{
+			return false;
+		}
+		return true;
+	}
+	
+	public static boolean parseSam(String arg, String a, String b){
+		if(a.equals("samversion") || a.equals("samv") || a.equals("sam")){
+			assert(b!=null) : "The sam flag requires a version number, e.g. 'sam=1.4'";
+			SamLine.VERSION=Float.parseFloat(b);
+		}else if(a.equals("sambamba")){
+			Data.USE_SAMBAMBA=Parse.parseBoolean(b);
+		}else if(a.equals("samtools")){
+			Data.USE_SAMTOOLS=Parse.parseBoolean(b);
+		}else if(a.equals("streamerthreads")){
+			SamStreamer.DEFAULT_THREADS=Integer.parseInt(b);
+		}else if(a.equals("prefermd") || a.equals("prefermdtag")){
+			SamLine.PREFER_MDTAG=Parse.parseBoolean(b);
+		}else if(a.equals("notags")){
+			SamLine.NO_TAGS=Parse.parseBoolean(b);
+		}else if(a.equals("mdtag") || a.equals("md")){
+			SamLine.MAKE_MD_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("idtag")){
+			SamLine.MAKE_IDENTITY_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("xmtag") || a.equals("xm")){
+			SamLine.MAKE_XM_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("smtag")){
+			SamLine.MAKE_SM_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("amtag")){
+			SamLine.MAKE_AM_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("nmtag")){
+			SamLine.MAKE_NM_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("stoptag")){
+			SamLine.MAKE_STOP_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("lengthtag")){
+			SamLine.MAKE_LENGTH_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("boundstag")){
+			SamLine.MAKE_BOUNDS_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("scoretag")){
+			SamLine.MAKE_SCORE_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("sortscaffolds")){
+			SamLine.SORT_SCAFFOLDS=Parse.parseBoolean(b);
+		}else if(a.equals("customtag")){
+			SamLine.MAKE_CUSTOM_TAGS=Parse.parseBoolean(b);
+		}else if(a.equals("nhtag")){
+			SamLine.MAKE_NH_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("keepnames")){
+			SamLine.KEEP_NAMES=Parse.parseBoolean(b);
+		}else if(a.equals("saa") || a.equals("secondaryalignmentasterisks")){
+			SamLine.SECONDARY_ALIGNMENT_ASTERISKS=Parse.parseBoolean(b);
+		}else if(a.equals("inserttag")){
+			SamLine.MAKE_INSERT_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("correctnesstag")){
+			SamLine.MAKE_CORRECTNESS_TAG=Parse.parseBoolean(b);
+		}else if(a.equals("intronlen") || a.equals("intronlength")){
+			SamLine.INTRON_LIMIT=Integer.parseInt(b);
+			SamLine.setintron=true;
+		}else if(a.equals("suppressheader") || a.equals("noheader")){
+			ReadStreamWriter.NO_HEADER=Parse.parseBoolean(b);
+		}else if(a.equals("noheadersequences") || a.equals("nhs") || a.equals("suppressheadersequences")){
+			ReadStreamWriter.NO_HEADER_SEQUENCES=Parse.parseBoolean(b);
+		}else if(a.equals("tophat")){
+			if(Parse.parseBoolean(b)){
+				SamLine.MAKE_TOPHAT_TAGS=true;
+				FastaReadInputStream.FAKE_QUALITY=true;
+				Shared.FAKE_QUAL=40;
+				SamLine.MAKE_MD_TAG=true;
+			}
+		}else if(a.equals("xstag") || a.equals("xs")){
+			SamLine.MAKE_XS_TAG=true;
+			if(b!=null){
+				b=b.toLowerCase();
+				if(b.startsWith("fr-")){b=b.substring(3);}
+				if(b.equals("ss") || b.equals("secondstrand")){
+					SamLine.XS_SECONDSTRAND=true;
+				}else if(b.equals("fs") || b.equals("firststrand")){
+					SamLine.XS_SECONDSTRAND=false;
+				}else if(b.equals("us") || b.equals("unstranded")){
+					SamLine.XS_SECONDSTRAND=false;
+				}else{
+					SamLine.MAKE_XS_TAG=Parse.parseBoolean(b);
+				}
+			}
+			SamLine.setxs=true;
+		}else if(a.equals("flipsam")){
+			SamLine.FLIP_ON_LOAD=Parse.parseBoolean(b);
+		}else if(parseReadgroup(arg, a, b)){
+			//do nothing
+		}else{
+			return false;
+		}
+		return true;
+	}
+
+	public static boolean parseFasta(String arg, String a, String b){
+		if(a.equals("fastareadlen") || a.equals("fastareadlength")){
+			FastaReadInputStream.TARGET_READ_LEN=Integer.parseInt(b);
+			FastaReadInputStream.SPLIT_READS=(FastaReadInputStream.TARGET_READ_LEN>0);
+		}else if(a.equals("fastaminread") || a.equals("fastaminlen") || a.equals("fastaminlength")){
+			FastaReadInputStream.MIN_READ_LEN=Integer.parseInt(b);
+		}else if(a.equals("forcesectionname")){
+			FastaReadInputStream.FORCE_SECTION_NAME=Parse.parseBoolean(b);
+		}else if(a.equals("fastawrap") || a.equals("wrap")){
+			Shared.FASTA_WRAP=Parse.parseIntKMG(b);
+		}else if(a.equals("fastadump")){
+			AbstractKmerTable.FASTA_DUMP=Parse.parseBoolean(b);
+		}else{
+			return false;
+		}
+		return true;
+	}
+	
+	public static boolean parseQualityAdjust(String arg, String a, String b){
+		int pass=0;
+		if(a.endsWith("_p1") || a.endsWith("_p2")){
+			pass=Integer.parseInt(a.substring(a.length()-1))-1;
+			a=a.substring(0, a.length()-3);
+		}
+		
+		if(a.equals("trackall")){
+			CalcTrueQuality.TRACK_ALL=Parse.parseBoolean(b);
+		}else if(a.equals("clearmatrices")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){
+				CalcTrueQuality.use_q102=new boolean[] {false, false};
+				CalcTrueQuality.use_qap=new boolean[] {false, false};
+				CalcTrueQuality.use_qbp=new boolean[] {false, false};
+				CalcTrueQuality.use_q10=new boolean[] {false, false};
+				CalcTrueQuality.use_q12=new boolean[] {false, false};
+				CalcTrueQuality.use_qb12=new boolean[] {false, false};
+				CalcTrueQuality.use_qb012=new boolean[] {false, false};
+				CalcTrueQuality.use_qb123=new boolean[] {false, false};
+				CalcTrueQuality.use_qb234=new boolean[] {false, false};
+				CalcTrueQuality.use_q12b12=new boolean[] {false, false};
+				CalcTrueQuality.use_qp=new boolean[] {false, false};
+				CalcTrueQuality.use_q=new boolean[] {false, false};
+			}
+		}else if(a.equals("loadq102")){
+			CalcTrueQuality.use_q102[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("loadqap")){
+			CalcTrueQuality.use_qap[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("loadqbp")){
+			CalcTrueQuality.use_qbp[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("loadq10")){
+			CalcTrueQuality.use_q10[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("loadq12")){
+			CalcTrueQuality.use_q12[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("loadqb12")){
+			CalcTrueQuality.use_qb12[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("loadqb012")){
+			CalcTrueQuality.use_qb012[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("loadqb123")){
+			CalcTrueQuality.use_qb123[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("loadqb234")){
+			CalcTrueQuality.use_qb234[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("loadq12b12")){
+			CalcTrueQuality.use_q12b12[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("loadqp")){
+			CalcTrueQuality.use_qp[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("loadq")){
+			CalcTrueQuality.use_q[pass]=Parse.parseBoolean(b);
+		}else if(a.equals("observationcutoff")){
+			long x=Parse.parseIntKMG(b);
+			CalcTrueQuality.OBSERVATION_CUTOFF[pass]=x;
+		}else if(a.equals("recalpasses")){
+			CalcTrueQuality.passes=Integer.parseInt(b);
+		}else if(a.equals("recalqmax")){
+			int x=Tools.mid(1, Integer.parseInt(b), 93);
+			CalcTrueQuality.setQmax(x);
+			Read.setMaxCalledQuality(Tools.max(x, Read.MAX_CALLED_QUALITY()));
+		}else if(a.equals("recalqmin")){
+			int x=Tools.mid(0, Integer.parseInt(b), 93);
+			Read.setMinCalledQuality(Tools.min(x, Read.MIN_CALLED_QUALITY()));
+		}else if(a.equals("recalwithposition") || a.equals("recalwithpos") || a.equals("recalusepos")){
+			boolean x=Parse.parseBoolean(b);
+			if(!x){
+				Arrays.fill(CalcTrueQuality.use_qp, false);
+				Arrays.fill(CalcTrueQuality.use_qbp, false);
+				Arrays.fill(CalcTrueQuality.use_qap, false);
+			}
+		}else if(a.equals("qmatrixmode")){
+			if("weighted".equalsIgnoreCase(b) || "weightedaverage".equalsIgnoreCase(b)){
+				CalcTrueQuality.USE_WEIGHTED_AVERAGE=true;
+			}else if("average".equalsIgnoreCase(b) || "avg".equalsIgnoreCase(b)){
+				CalcTrueQuality.USE_WEIGHTED_AVERAGE=false;
+				CalcTrueQuality.USE_AVERAGE=true;
+			}else if("max".equalsIgnoreCase(b)){
+				CalcTrueQuality.USE_AVERAGE=CalcTrueQuality.USE_WEIGHTED_AVERAGE=false;
+			}
+		}else{
+			return false;
+		}
+		return true;
+	}
+
+	static boolean isJavaFlag(String arg){
+		if(arg==null){return false;}
+		if(arg.startsWith("-Xmx") || arg.startsWith("-Xms") || arg.startsWith("-Xmn") || arg.startsWith("-xmx") || arg.startsWith("-xms") || arg.startsWith("-xmn")){
+			return arg.length()>4 && Tools.isDigit(arg.charAt(4));
+		}
+		if(arg.startsWith("Xmx") || arg.startsWith("Xms") || arg.startsWith("Xmn") || arg.startsWith("xmx")){
+			return arg.length()>3 && (Tools.isDigit(arg.charAt(3)) || arg.charAt(3)=='=');
+		}
+		if(arg.equals("-ea") || arg.equals("-da") || arg.equals("ea") || arg.equals("da")){
+			return true;
+		}
+		if(arg.equals("ExitOnOutOfMemoryError") || arg.equals("exitonoutofmemoryerror") || arg.equals("eoom")){return true;}
+		if(arg.equals("-ExitOnOutOfMemoryError") || arg.equals("-exitonoutofmemoryerror") || arg.equals("-eoom")){return true;}
+		
+		return false;
+	}
+	
+	/** Return true if the user seems confused */
+	static boolean parseHelp(String[] args, boolean autoExit){
+		if(args==null || args.length==0 || (args.length==1 && args[0]==null)){
+			if(autoExit){printHelp(1);}
+			return true;
+		}
+		
+		final String s=args[args.length-1].toLowerCase();
+		
+		if(s.equals("-version") || s.equals("--version") || (s.equals("version") && !new File(s).exists())){
+			if(autoExit){printHelp(0);}
+			return true;
+		}else if(s.equals("-h") || s.equals("-help") || s.equals("--help")
+				|| s.equals("?") || s.equals("-?") || (s.equals("help") && !new File(s).exists())){
+			if(autoExit){printHelp(0);}
+			return true;
+		}
+		return false;
+	}
+	
+	public static void printHelp(int exitCode){
+		System.err.println("BBMap version "+Shared.BBMAP_VERSION_STRING);
+		System.err.println("For help, please run the shellscript with no parameters, or look in /docs/.");
+		System.exit(exitCode);
+	}
+	
+	/** Set SamLine Readgroup Strings */
+	public static boolean parseReadgroup(String arg, String a, String b){
+		if(a.equals("readgroup") || a.equals("readgroupid") || a.equals("rgid")){
+			SamLine.READGROUP_ID=b;
+			if(b!=null){SamLine.READGROUP_TAG="RG:Z:"+b;}
+		}else if(a.equals("readgroupcn") || a.equals("rgcn")){
+			SamLine.READGROUP_CN=b;
+		}else if(a.equals("readgroupds") || a.equals("rgds")){
+			SamLine.READGROUP_DS=b;
+		}else if(a.equals("readgroupdt") || a.equals("rgdt")){
+			SamLine.READGROUP_DT=b;
+		}else if(a.equals("readgroupfo") || a.equals("rgfo")){
+			SamLine.READGROUP_FO=b;
+		}else if(a.equals("readgroupks") || a.equals("rgks")){
+			SamLine.READGROUP_KS=b;
+		}else if(a.equals("readgrouplb") || a.equals("rglb")){
+			SamLine.READGROUP_LB=b;
+		}else if(a.equals("readgrouppg") || a.equals("rgpg")){
+			SamLine.READGROUP_PG=b;
+		}else if(a.equals("readgrouppi") || a.equals("rgpi")){
+			SamLine.READGROUP_PI=b;
+		}else if(a.equals("readgrouppl") || a.equals("rgpl")){
+			SamLine.READGROUP_PL=b;
+		}else if(a.equals("readgrouppu") || a.equals("rgpu")){
+			SamLine.READGROUP_PU=b;
+		}else if(a.equals("readgroupsm") || a.equals("rgsm")){
+			SamLine.READGROUP_SM=b;
+		}else{
+			return false;
+		}
+		return true;
+	}
+	
+	/** Fix Readgroup Strings */
+	public static void postparseReadgroup(String fname){
+		if(fname==null){return;}
+		fname=ReadWrite.stripToCore(fname);
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_ID)){
+			SamLine.READGROUP_ID=fname;
+			if(fname!=null){SamLine.READGROUP_TAG="RG:Z:"+fname;}
+		}
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_CN)){
+			SamLine.READGROUP_CN=fname;
+		}
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_DS)){
+			SamLine.READGROUP_DS=fname;
+		}
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_DT)){
+			SamLine.READGROUP_DT=fname;
+		}
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_FO)){
+			SamLine.READGROUP_FO=fname;
+		}
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_KS)){
+			SamLine.READGROUP_KS=fname;
+		}
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_LB)){
+			SamLine.READGROUP_LB=fname;
+		}
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_PG)){
+			SamLine.READGROUP_PG=fname;
+		}
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_PI)){
+			SamLine.READGROUP_PI=fname;
+		}
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_PL)){
+			SamLine.READGROUP_PL=fname;
+		}
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_PU)){
+			SamLine.READGROUP_PU=fname;
+		}
+		if("filename".equalsIgnoreCase(SamLine.READGROUP_SM)){
+			SamLine.READGROUP_SM=fname;
+		}
+	}
+	
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	public float trimE(){
+		return (float)QualityTools.phredToProbError(trimq);
+	}
+	
+	public float[] trimE2(){
+		return QualityTools.phredToProbError(trimq2==null ? new float[] {trimq} : trimq2);
+	}
+
+	public boolean loglog=false;
+	public boolean loglogOut=false;
+	public int loglogbuckets=2048;//1999
+	public int loglogbits=8;
+	public int loglogk=31;
+	public long loglogseed=-1;
+	public float loglogMinprob=0;
+	public IntList loglogKlist=new IntList();
+	
+	public boolean recalibrateQuality=false;
+	
+	public int forceTrimModulo=-1;
+	public int forceTrimLeft=-1;
+	public int forceTrimRight=-1;
+	public int forceTrimRight2=-1;
+	public int build=1;
+
+	public long maxReads=-1;
+	public float samplerate=1f;
+	public long sampleseed=-1;
+
+	public boolean qtrimLeft=false;
+	public boolean qtrimRight=false;
+	public boolean trimClip=false;
+	public int trimPolyA=0;
+	
+	public int trimPolyGLeft=0;
+	public int trimPolyGRight=0;
+	public int filterPolyG=0;
+	
+	public int trimPolyCLeft=0;
+	public int trimPolyCRight=0;
+	public int filterPolyC=0;
+
+	public boolean qtrim1=false;
+	public boolean qtrim2=false;
+
+	public float trimq=6;
+	public float[] trimq2=null;
+	public float minAvgQuality=0;
+	public byte minBaseQuality=0;
+	public int minAvgQualityBases=0;
+	public int maxNs=-1;
+	public int minConsecutiveBases=0;
+	public int minReadLength=0;
+	public int maxReadLength=-1;
+	public int minTrimLength=-1;
+	public float minLenFraction=0;
+	public float minGC=0;
+	public float maxGC=1;
+	public boolean usePairGC=true;
+//	public boolean filterGC=false;
+	public boolean untrim=false;
+	public boolean tossJunk=false;
+
+	public float minIdFilter=-1;
+	public float maxIdFilter=999999999;
+	public int subfilter=-1;
+	public int clipfilter=-1;
+	public int delfilter=-1;
+	public int insfilter=-1;
+	public int indelfilter=-1;
+	public int dellenfilter=-1;
+	public int inslenfilter=-1;
+	public int editfilter=-1;
+	public int nfilter=-1;
+	
+	public int breakLength=0;
+	/** Toss pair only if both reads are shorter than limit */
+	public boolean requireBothBad=false;
+	public boolean trimBadSequence=false;
+	public boolean chastityFilter=false;
+	public boolean removeBadBarcodes=false;
+	public boolean failBadBarcodes=false;
+	public boolean failIfNoBarcode=false;
+	
+	public HashSet<String> barcodes=null;
+	
+	/** Permission to overwrite existing files */
+	public boolean overwrite=false;
+	
+	/** Permission to append to existing files */
+	public boolean append=false;
+	public boolean testsize=false;
+	
+	/** Whether input file interleaving was explicitly set */
+	public boolean setInterleaved=false;
+	
+	public String in1=null;
+	public String in2=null;
+	
+	public String qfin1=null;
+	public String qfin2=null;
+
+	public String out1=null;
+	public String out2=null;
+	public String outsingle=null;
+	public boolean setOut=false;
+
+	public String qfout1=null;
+	public String qfout2=null;
+	
+	public String extin=null;
+	public String extout=null;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Static Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public static String loglogType="LogLog2";
+	public static boolean silent=false;
+	
+	private static boolean setTrimRname=false;
+	private static byte qin=-1;
+	private static byte qout=-1;
+	private static boolean parsedQuality=false;
+	
+	public static void setQuality(int x){
+		qin=(byte)x;
+		parsedQuality=(x>-1);
+	}
+	public static void processQuality(){
+//		assert(parsedQuality);
+		if(!parsedQuality){return;}
+		if(qin!=-1 && qout!=-1){
+			FASTQ.ASCII_OFFSET=qin;
+			FASTQ.ASCII_OFFSET_OUT=qout;
+			FASTQ.DETECT_QUALITY=false;
+		}else if(qin!=-1){
+			FASTQ.ASCII_OFFSET=qin;
+			FASTQ.DETECT_QUALITY=false;
+		}else if(qout!=-1){
+			FASTQ.ASCII_OFFSET_OUT=qout;
+			FASTQ.DETECT_QUALITY_OUT=false;
+		}
+	}
+
+	public boolean validateStdio(FileFormat... ffa) {
+		boolean b=true;
+		for(FileFormat ff:ffa){
+			b=validateStdio(ff)&b;
+		}
+		return b;
+	}
+
+	public boolean validateStdio(FileFormat ff) {
+		if(ff==null || !ff.stdio()){return true;}
+		if(ff.fastq() && ff.stdin()){
+			assert(setInterleaved) : "\nERROR: When piping fastq data from stdin, interleaving must be explicitly stated\n"
+					+ "with the flag int=f for unpaired data or int=t for paired data.\n";
+		}
+		final int ext=ff.rawExtensionCode();
+		if(ff.stdout() && ext==FileFormat.UNKNOWN){
+			assert(false) : "\nERROR: When piping reads to stdout, the output format must be specified with an extension,\n"
+					+ "such as stdout.fq or stdout.sam.gz.\n";
+		}
+		if(ff.stdin() && ext==FileFormat.UNKNOWN){
+			assert(false) : "\nERROR: When piping reads from stdin, the input format should be specified with an extension,\n"
+					+ "such as stdin.fq or stdin.sam.gz.\n";
+		}
+		return true;
+	}
+	
+}