package shared;

import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;

import align2.QualityTools;
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.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=Tools.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=Tools.parseBoolean(b);
		}else if(a.equals("overwrite") || a.equals("ow")){
			overwrite=Tools.parseBoolean(b);
		}else if(a.equals("testsize")){
			testsize=Tools.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=Tools.parseBoolean(b);
		}else if(a.equals("silent")){
			silent=Tools.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=Tools.parseBoolean(b);
				}
			}else{
				loglog=Tools.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=Tools.parseBoolean(b);
				}
			}else{
				loglogOut=Tools.parseBoolean(b);
			}
		}else if(a.equals("buckets") || a.equals("loglogbuckets")){
			loglogbuckets=Integer.parseInt(b);
		}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{
			return false;
		}
		return true;
	}
	
	public boolean parseInterleaved(String arg, String a, String b){
		if(a.equals("testinterleaved")){
			FASTQ.TEST_INTERLEAVED=Tools.parseBoolean(b);
			System.err.println("Set TEST_INTERLEAVED to "+FASTQ.TEST_INTERLEAVED);
			setInterleaved=true;
		}else if(a.equals("forceinterleaved")){
			FASTQ.FORCE_INTERLEAVED=Tools.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=Tools.parseBoolean(b);
				System.err.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
				setInterleaved=true;
			}
		}else if(a.equals("overrideinterleaved")){
			boolean x=Tools.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=Tools.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=Tools.parseBoolean(b);
			}
		}else if(a.equals("trimgoodinterval")){
			TrimRead.minGoodInterval=Integer.parseInt(b);
		}else if(a.equals("trimright") || a.equals("qtrimright")){
			qtrimRight=Tools.parseBoolean(b);
		}else if(a.equals("trimleft") || a.equals("qtrimleft")){
			qtrimLeft=Tools.parseBoolean(b);
		}else if(a.equals("trimq") || a.equals("trimquality") || a.equals("trimq2")){
			parseTrimq(a, b);
		}else if(a.equals("trimclip")){
			trimClip=Tools.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=Tools.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=Tools.parseBoolean(b);
		}else if(a.equals("chastityfilter") || a.equals("cf")){
			chastityFilter=Tools.parseBoolean(b);
		}else if(a.equals("failnobarcode")){
			failIfNoBarcode=Tools.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=Tools.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=Tools.parseBoolean(b);
		}else if(a.equals("removeifeitherbad") || a.equals("rieb")){
			requireBothBad=!Tools.parseBoolean(b);
		}else if(a.equals("ml") || a.equals("minlen") || a.equals("minlength")){
			minReadLength=Tools.parseIntKMG(b);
		}else if(a.equals("maxlength") || a.equals("maxreadlength") || a.equals("maxreadlen") || a.equals("maxlen")){
			maxReadLength=Tools.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=Tools.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=Tools.parseBoolean(b);
		}else if(a.equals("mintl") || a.equals("mintrimlen") || a.equals("mintrimlength")){
			minTrimLength=Integer.parseInt(b);
		}else if(a.equals("untrim")){
			untrim=Tools.parseBoolean(b);
		}else if(a.equals("tossjunk")){
			boolean x=Tools.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")){
			idFilter=Float.parseFloat(b);
			if(idFilter>1f){idFilter/=100;}
			assert(idFilter<=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(Tools.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(Tools.parseBoolean(b)){
				KillSwitch.launch();
			}
		}else if(a.equals("trd") || a.equals("trc") || a.equals("trimreaddescription") || a.equals("trimreaddescriptions")){
			Shared.TRIM_READ_COMMENTS=Tools.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=Tools.parseBoolean(b);
			setTrimRname=true;
		}else if(a.equals("tuc") || a.equals("touppercase")){
			Read.TO_UPPER_CASE=Tools.parseBoolean(b);
		}else if(a.equals("lctn") || a.equals("lowercaseton")){
			Read.LOWER_CASE_TO_N=Tools.parseBoolean(b);
		}else if(a.equals("changequality") || a.equals("cq")){
			Read.CHANGE_QUALITY=Tools.parseBoolean(b);
			BBMerge.changeQuality=Read.CHANGE_QUALITY;
		}else if(a.equals("tossbrokenreads") || a.equals("tbr")){
			boolean x=Tools.parseBoolean(b);
			Read.TOSS_BROKEN_QUALITY=x;
			ConcurrentReadInputStream.REMOVE_DISCARDED_READS=x;
		}else if(a.equals("nullifybrokenquality") || a.equals("nbq")){
			boolean x=Tools.parseBoolean(b);
			Read.NULLIFY_BROKEN_QUALITY=x;
		}else if(a.equals("dotdashxton")){
			boolean x=Tools.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{assert(false) : "Bad junk mode: "+arg;}
		}else if(a.equals("ignorejunk")){
			boolean x=Tools.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=Tools.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=Tools.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=Tools.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=Tools.parseBoolean(b);
		}else if(a.equals("validatebranchless")){
//			Read.VALIDATE_BRANCHLESS=Tools.parseBoolean(b);
		}else if(a.equals("bf1")){
			ByteFile.FORCE_MODE_BF1=Tools.parseBoolean(b);
			ByteFile.FORCE_MODE_BF2=!ByteFile.FORCE_MODE_BF1;
		}else if(a.equals("bf1bufferlen")){
			ByteFile1.bufferlen=(int)Tools.parseKMGBinary(b);
		}else if(a.equals("utot")){
			Read.U_TO_T=Tools.parseBoolean(b);
		}else if(a.equals("bf2")){
			ByteFile.FORCE_MODE_BF2=Tools.parseBoolean(b);
			ByteFile.FORCE_MODE_BF1=!ByteFile.FORCE_MODE_BF2;
		}else if(a.equals("bf3")){
			ByteFile.FORCE_MODE_BF3=Tools.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=Tools.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=Tools.parseBoolean(b);
			}
		}else if(a.equals("crismpi")){
			Shared.USE_CRISMPI=Tools.parseBoolean(b);
		}else if(a.equals("mpikeepall")){
			Shared.MPI_KEEP_ALL=Tools.parseBoolean(b);
		}else if(a.equals("readbufferlength") || a.equals("readbufferlen")){
			Shared.setBufferLen((int)Tools.parseKMG(b));
		}else if(a.equals("readbufferdata")){
			Shared.setBufferData(Tools.parseKMG(b));
		}else if(a.equals("readbuffers")){
			Shared.setBuffers(Integer.parseInt(b));
		}else if(a.equals("rbm") || a.equals("renamebymapping")){
			FASTQ.TAG_CUSTOM=Tools.parseBoolean(b);
		}else if(a.equals("don") || a.equals("deleteoldname")){
			FASTQ.DELETE_OLD_NAME=Tools.parseBoolean(b);
		}else if(a.equals("assertcigar")){
			ReadStreamWriter.ASSERT_CIGAR=Tools.parseBoolean(b);
		}else if(a.equals("verbosesamline")){
			SamLine.verbose=Tools.parseBoolean(b);
		}else if(a.equals("parsecustom") || a.equals("fastqparsecustom")){
			FASTQ.PARSE_CUSTOM=Tools.parseBoolean(b);
			System.err.println("Set FASTQ.PARSE_CUSTOM to "+FASTQ.PARSE_CUSTOM);
		}else if(a.equals("fairqueues")){
			ConcurrentDepot.fair=Tools.parseBoolean(b);
		}else if(a.equals("fixheader") || a.equals("fixheaders")){
			Read.FIX_HEADER=Tools.parseBoolean(b);
		}else if(a.equals("allownullheader") || a.equals("allownullheaders")){
			Read.ALLOW_NULL_HEADER=Tools.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=Tools.parseBoolean(b);
		}else if(a.equals("amino8")){
			SketchObject.amino8=Tools.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);
			System.err.println("Set threads to "+Shared.threads());
		}else if(a.equals("recalpairnum") || a.equals("recalibratepairnum")){
			CalcTrueQuality.USE_PAIRNUM=Tools.parseBoolean(b);
		}else if(a.equals("taxpath")){
			TaxTree.TAX_PATH=b.replaceAll("\\\\", "/");
		}else if(a.equals("parallelsort")){
			boolean x=Tools.parseBoolean(b);
			Shared.setParallelSort(x);
		}else if(a.equals("gcbeforemem")){
			Shared.GC_BEFORE_PRINT_MEMORY=Tools.parseBoolean(b);
		}else if(a.equals("warnifnosequence")){
			FastaReadInputStream.WARN_IF_NO_SEQUENCE=Tools.parseBoolean(b);
		}else if(a.equals("warnfirsttimeonly")){
			FastaReadInputStream.WARN_FIRST_TIME_ONLY=Tools.parseBoolean(b);
		}else if(a.equals("silva")){
			TaxTree.SILVA_MODE=Tools.parseBoolean(b);
		}else if(a.equals("parallelsort") || a.equals("paralellsort")){
			Shared.parallelSort=Tools.parseBoolean(b);
		}else if(a.equals("imghq")){
			TaxTree.IMG_HQ=Tools.parseBoolean(b);
		}
		
		else if(a.equals("callins") ||  a.equals("callinss")){
			var2.Var.CALL_INS=Tools.parseBoolean(b);
		}else if(a.equals("calldel") || a.equals("calldels")){
			var2.Var.CALL_DEL=Tools.parseBoolean(b);
		}else if(a.equals("callsub") || a.equals("callsubs") || a.equals("callsnp") || a.equals("callsnps")){
			var2.Var.CALL_SUB=Tools.parseBoolean(b);
		}else if(a.equals("callindel") || a.equals("callindels")){
			var2.Var.CALL_INS=var2.Var.CALL_DEL=Tools.parseBoolean(b);
		}else if(a.equals("calljunct") || a.equals("calljunction") || a.equals("calljunctions")){
			var2.Var.CALL_JUNCTION=Tools.parseBoolean(b);
		}else if(a.equals("callnocall") || a.equals("callnocalls")){
			var2.Var.CALL_NOCALL=Tools.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=Tools.parseBoolean(b);
		}
		
		else if(a.equals("2passresize") || a.equals("twopassresize")){
			AbstractKmerTable.TWO_PASS_RESIZE=Tools.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=Tools.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=Tools.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=Tools.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=Tools.parseIntKMG(b);
		}
		
		else if(a.equals("fixindels") || a.equals("ignorevcfindels")){
			CallVariants.fixIndels=Tools.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=Tools.parseBoolean(b);
		}else if(a.equals("usegzip") || a.equals("gzip")){
			ReadWrite.USE_GZIP=Tools.parseBoolean(b);
		}else if(a.equals("usebgzip") || a.equals("bgzip")){
			ReadWrite.USE_BGZIP=Tools.parseBoolean(b);
		}else if(a.equals("forcepigz")){
			ReadWrite.FORCE_PIGZ=Tools.parseBoolean(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=Tools.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=Tools.parseBoolean(b);
		}else if(a.equals("useunpigz") || a.equals("unpigz")){
			ReadWrite.USE_UNPIGZ=Tools.parseBoolean(b);
		}else if(a.equals("usebzip2") || a.equals("bzip2")){
			ReadWrite.USE_BZIP2=Tools.parseBoolean(b);
		}else if(a.equals("usepbzip2") || a.equals("pbzip2")){
			ReadWrite.USE_PBZIP2=Tools.parseBoolean(b);
		}else if(a.equals("uselbzip2") || a.equals("lbzip2")){
			ReadWrite.USE_LBZIP2=Tools.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("streamerthreads")){
			SamStreamer.DEFAULT_THREADS=Integer.parseInt(b);
		}else if(a.equals("prefermd") || a.equals("prefermdtag")){
			SamLine.PREFER_MDTAG=Tools.parseBoolean(b);
		}else if(a.equals("notags")){
			SamLine.NO_TAGS=Tools.parseBoolean(b);
		}else if(a.equals("mdtag") || a.equals("md")){
			SamLine.MAKE_MD_TAG=Tools.parseBoolean(b);
		}else if(a.equals("idtag")){
			SamLine.MAKE_IDENTITY_TAG=Tools.parseBoolean(b);
		}else if(a.equals("xmtag") || a.equals("xm")){
			SamLine.MAKE_XM_TAG=Tools.parseBoolean(b);
		}else if(a.equals("smtag")){
			SamLine.MAKE_SM_TAG=Tools.parseBoolean(b);
		}else if(a.equals("amtag")){
			SamLine.MAKE_AM_TAG=Tools.parseBoolean(b);
		}else if(a.equals("nmtag")){
			SamLine.MAKE_NM_TAG=Tools.parseBoolean(b);
		}else if(a.equals("stoptag")){
			SamLine.MAKE_STOP_TAG=Tools.parseBoolean(b);
		}else if(a.equals("lengthtag")){
			SamLine.MAKE_LENGTH_TAG=Tools.parseBoolean(b);
		}else if(a.equals("boundstag")){
			SamLine.MAKE_BOUNDS_TAG=Tools.parseBoolean(b);
		}else if(a.equals("scoretag")){
			SamLine.MAKE_SCORE_TAG=Tools.parseBoolean(b);
		}else if(a.equals("sortscaffolds")){
			SamLine.SORT_SCAFFOLDS=Tools.parseBoolean(b);
		}else if(a.equals("customtag")){
			SamLine.MAKE_CUSTOM_TAGS=Tools.parseBoolean(b);
		}else if(a.equals("nhtag")){
			SamLine.MAKE_NH_TAG=Tools.parseBoolean(b);
		}else if(a.equals("keepnames")){
			SamLine.KEEP_NAMES=Tools.parseBoolean(b);
		}else if(a.equals("saa") || a.equals("secondaryalignmentasterisks")){
			SamLine.SECONDARY_ALIGNMENT_ASTERISKS=Tools.parseBoolean(b);
		}else if(a.equals("inserttag")){
			SamLine.MAKE_INSERT_TAG=Tools.parseBoolean(b);
		}else if(a.equals("correctnesstag")){
			SamLine.MAKE_CORRECTNESS_TAG=Tools.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=Tools.parseBoolean(b);
		}else if(a.equals("noheadersequences") || a.equals("nhs") || a.equals("suppressheadersequences")){
			ReadStreamWriter.NO_HEADER_SEQUENCES=Tools.parseBoolean(b);
		}else if(a.equals("tophat")){
			if(Tools.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=Tools.parseBoolean(b);
				}
			}
			SamLine.setxs=true;
		}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=Tools.parseBoolean(b);
		}else if(a.equals("fastawrap")){
			Shared.FASTA_WRAP=Tools.parseIntKMG(b);
		}else if(a.equals("fastadump")){
			AbstractKmerTable.FASTA_DUMP=Tools.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=Tools.parseBoolean(b);
		}else if(a.equals("clearmatrices")){
			boolean x=Tools.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]=Tools.parseBoolean(b);
		}else if(a.equals("loadqap")){
			CalcTrueQuality.use_qap[pass]=Tools.parseBoolean(b);
		}else if(a.equals("loadqbp")){
			CalcTrueQuality.use_qbp[pass]=Tools.parseBoolean(b);
		}else if(a.equals("loadq10")){
			CalcTrueQuality.use_q10[pass]=Tools.parseBoolean(b);
		}else if(a.equals("loadq12")){
			CalcTrueQuality.use_q12[pass]=Tools.parseBoolean(b);
		}else if(a.equals("loadqb12")){
			CalcTrueQuality.use_qb12[pass]=Tools.parseBoolean(b);
		}else if(a.equals("loadqb012")){
			CalcTrueQuality.use_qb012[pass]=Tools.parseBoolean(b);
		}else if(a.equals("loadqb123")){
			CalcTrueQuality.use_qb123[pass]=Tools.parseBoolean(b);
		}else if(a.equals("loadqb234")){
			CalcTrueQuality.use_qb234[pass]=Tools.parseBoolean(b);
		}else if(a.equals("loadq12b12")){
			CalcTrueQuality.use_q12b12[pass]=Tools.parseBoolean(b);
		}else if(a.equals("loadqp")){
			CalcTrueQuality.use_qp[pass]=Tools.parseBoolean(b);
		}else if(a.equals("loadq")){
			CalcTrueQuality.use_q[pass]=Tools.parseBoolean(b);
		}else if(a.equals("observationcutoff")){
			long x=Tools.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=Tools.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;
	}
	
	
	/*--------------------------------------------------------------*/
	/*----------------            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 idFilter=-1;
	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;
	
	public boolean overwrite=false;
	public boolean append=false;
	public boolean testsize=false;
	
	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;
	
	public boolean silent=false;
	
	/*--------------------------------------------------------------*/
	/*----------------        Static Fields         ----------------*/
	/*--------------------------------------------------------------*/
	
	private static boolean setTrimRname=false;
	private static byte qin=-1;
	private static byte qout=-1;
	private static boolean parsedQuality=false;
	
	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;
	}
	
}
