jpayne@68: package consensus;
jpayne@68: 
jpayne@68: import java.io.PrintStream;
jpayne@68: import java.util.ArrayList;
jpayne@68: import java.util.LinkedHashMap;
jpayne@68: import java.util.Map.Entry;
jpayne@68: 
jpayne@68: import fileIO.ByteFile;
jpayne@68: import fileIO.ByteStreamWriter;
jpayne@68: import fileIO.FileFormat;
jpayne@68: import fileIO.ReadWrite;
jpayne@68: import prok.ProkObject;
jpayne@68: import shared.Parse;
jpayne@68: import shared.Parser;
jpayne@68: import shared.PreParser;
jpayne@68: import shared.ReadStats;
jpayne@68: import shared.Shared;
jpayne@68: import shared.Timer;
jpayne@68: import shared.Tools;
jpayne@68: import sketch.SketchObject;
jpayne@68: import stream.ConcurrentReadInputStream;
jpayne@68: import stream.ConcurrentReadOutputStream;
jpayne@68: import stream.FASTQ;
jpayne@68: import stream.FastaReadInputStream;
jpayne@68: import stream.Read;
jpayne@68: import stream.SamLine;
jpayne@68: import stream.SamReadStreamer;
jpayne@68: import stream.SamStreamer;
jpayne@68: import structures.ByteBuilder;
jpayne@68: import structures.ListNum;
jpayne@68: import template.Accumulator;
jpayne@68: import template.ThreadWaiter;
jpayne@68: import var2.Realigner;
jpayne@68: import var2.SamFilter;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * Alters a reference to represent the consensus of aligned reads.
jpayne@68:  * 
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date September 6, 1019
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class ConsensusMaker extends ConsensusObject implements Accumulator<ConsensusMaker.ProcessThread> {
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Initialization        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * Code entrance from the command line.
jpayne@68: 	 * @param args Command line arguments
jpayne@68: 	 */
jpayne@68: 	public static void main(String[] args){
jpayne@68: 		//Start a timer immediately upon code entrance.
jpayne@68: 		Timer t=new Timer();
jpayne@68: 		
jpayne@68: 		//Create an instance of this class
jpayne@68: 		ConsensusMaker x=new ConsensusMaker(args);
jpayne@68: 		
jpayne@68: 		//Run the object
jpayne@68: 		x.process(t);
jpayne@68: 		
jpayne@68: 		//Close the print stream if it was redirected
jpayne@68: 		Shared.closeStream(x.outstream);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * Constructor.
jpayne@68: 	 * @param args Command line arguments
jpayne@68: 	 */
jpayne@68: 	public ConsensusMaker(String[] args){
jpayne@68: 		
jpayne@68: 		{//Preparse block for help, config files, and outstream
jpayne@68: 			PreParser pp=new PreParser(args, getClass(), false);
jpayne@68: 			args=pp.args;
jpayne@68: 			outstream=pp.outstream;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Set shared static variables prior to parsing
jpayne@68: 		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
jpayne@68: 		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
jpayne@68: 		FASTQ.TEST_INTERLEAVED=FASTQ.FORCE_INTERLEAVED=false;
jpayne@68: 		
jpayne@68: 		samFilter.includeUnmapped=false;
jpayne@68: //		samFilter.includeSupplimentary=false;
jpayne@68: //		samFilter.includeDuplicate=false;
jpayne@68: 		samFilter.includeNonPrimary=false;
jpayne@68: 		samFilter.includeQfail=false;
jpayne@68: //		samFilter.minMapq=4;
jpayne@68: 		
jpayne@68: 		{//Parse the arguments
jpayne@68: 			final Parser parser=parse(args);
jpayne@68: 			
jpayne@68: 			Parser.processQuality();
jpayne@68: 			
jpayne@68: 			maxReads=parser.maxReads;
jpayne@68: 			overwrite=ReadStats.overwrite=parser.overwrite;
jpayne@68: 			append=ReadStats.append=parser.append;
jpayne@68: 			
jpayne@68: 			in=parser.in1;
jpayne@68: 			extin=parser.extin;
jpayne@68: 
jpayne@68: 			out=parser.out1;
jpayne@68: 			extout=parser.extout;
jpayne@68: 			silent=Parser.silent;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		{
jpayne@68: //			if("auto".equalsIgnoreCase(atomic)){Scaffold.setCA3A(Shared.threads()>8);}
jpayne@68: //			else{Scaffold.setCA3A(Parse.parseBoolean(atomic));}
jpayne@68: 
jpayne@68: 			if(ploidy<1){System.err.println("WARNING: ploidy not set; assuming ploidy=1."); ploidy=1;}
jpayne@68: 			samFilter.setSamtoolsFilter();
jpayne@68: 			
jpayne@68: 			streamerThreads=Tools.max(1, Tools.min(streamerThreads, Shared.threads()));
jpayne@68: 			assert(streamerThreads>0) : streamerThreads;
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		validateParams();
jpayne@68: 		fixExtensions(); //Add or remove .gz or .bz2 as needed
jpayne@68: 		checkFileExistence(); //Ensure files can be read and written
jpayne@68: 		checkStatics(); //Adjust file-related static fields as needed for this program 
jpayne@68: 		
jpayne@68: 		//Create output FileFormat objects
jpayne@68: 		ffout=FileFormat.testOutput(out, FileFormat.FASTA, extout, true, overwrite, append, ordered);
jpayne@68: 		ffmodel=FileFormat.testOutput(outModel, FileFormat.ALM, null, true, overwrite, false, ordered);
jpayne@68: 		
jpayne@68: 		//Create input FileFormat objects
jpayne@68: 		ffin=FileFormat.testInput(in, FileFormat.SAM, extin, true, true);
jpayne@68: 		ffref=FileFormat.testInput(ref, FileFormat.FASTA, null, true, true);
jpayne@68: 		
jpayne@68: 		if(inModelFile!=null){
jpayne@68: 			ArrayList<BaseGraph> list=(ArrayList<BaseGraph>)ReadWrite.readObject(inModelFile, false);
jpayne@68: 			inModel=list.get(0);
jpayne@68: 			inModel.calcProbs();
jpayne@68: 			inModel.makeWeights();
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------    Initialization Helpers    ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** Parse arguments from the command line */
jpayne@68: 	private Parser parse(String[] args){
jpayne@68: 		
jpayne@68: 		//Create a parser object
jpayne@68: 		Parser parser=new Parser();
jpayne@68: 		
jpayne@68: 		//Set any necessary Parser defaults here
jpayne@68: 		//parser.foo=bar;
jpayne@68: 		
jpayne@68: 		//Parse each argument
jpayne@68: 		for(int i=0; i<args.length; i++){
jpayne@68: 			String arg=args[i];
jpayne@68: 			
jpayne@68: 			//Break arguments into their constituent parts, in the form of "a=b"
jpayne@68: 			String[] split=arg.split("=");
jpayne@68: 			String a=split[0].toLowerCase();
jpayne@68: 			String b=split.length>1 ? split[1] : null;
jpayne@68: 			if(b!=null && b.equalsIgnoreCase("null")){b=null;}
jpayne@68: 			
jpayne@68: 			if(a.equals("verbose")){
jpayne@68: 				verbose=Parse.parseBoolean(b);
jpayne@68: 				BaseGraph.verbose=verbose;
jpayne@68: 			}else if(a.equals("ref")){
jpayne@68: 				ref=b;
jpayne@68: 			}else if(a.equals("outm") || a.equals("outmodel") || a.equals("model") || a.equals("alm")){
jpayne@68: 				outModel=b;
jpayne@68: 			}else if(a.equals("inm") || a.equals("inmodel")){
jpayne@68: 				inModelFile=b;
jpayne@68: 			}else if(a.equals("hist") || a.equals("histogram")){
jpayne@68: 				outHistFile=b;
jpayne@68: 			}else if(a.equals("realign")){
jpayne@68: 				realign=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("printscores")){
jpayne@68: 				printScores=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equalsIgnoreCase("useMapq")){
jpayne@68: 				useMapq=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equalsIgnoreCase("identityCeiling") || a.equalsIgnoreCase("idceiling") || a.equalsIgnoreCase("ceiling")){
jpayne@68: 				double d=Double.parseDouble(b);
jpayne@68: 				if(d<=2){d=d*100;}
jpayne@68: 				identityCeiling=(int)d;
jpayne@68: 				invertIdentity=true;
jpayne@68: 			}else if(a.equalsIgnoreCase("invertIdentity")){
jpayne@68: 				invertIdentity=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("name") || a.equals("rename") || a.equals("header")){
jpayne@68: 				name=b;
jpayne@68: 			}else if(a.equals("noindels")){
jpayne@68: 				noIndels=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equalsIgnoreCase("onlyConvertNs") || a.equalsIgnoreCase("nOnly") || a.equalsIgnoreCase("onlyN")){
jpayne@68: 				onlyConvertNs=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("ploidy")){
jpayne@68: 				ploidy=Integer.parseInt(b);
jpayne@68: 			}else if(a.equals("mindepth")){
jpayne@68: 				minDepth=Integer.parseInt(b);
jpayne@68: 			}else if(a.equals("trimdepth") || a.equals("trimdepthfraction")){
jpayne@68: 				trimDepthFraction=Float.parseFloat(b);
jpayne@68: 			}else if(a.equalsIgnoreCase("trimNs")){
jpayne@68: 				trimNs=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equalsIgnoreCase("mafn") || a.equals("mafnoref")){
jpayne@68: 				MAF_noref=Float.parseFloat(b);
jpayne@68: 			}else if(a.equalsIgnoreCase("mafsub")){
jpayne@68: 				MAF_sub=Float.parseFloat(b);
jpayne@68: 			}else if(a.equalsIgnoreCase("mafdel")){
jpayne@68: 				MAF_del=Float.parseFloat(b);
jpayne@68: 			}else if(a.equalsIgnoreCase("mafins")){
jpayne@68: 				MAF_ins=Float.parseFloat(b);
jpayne@68: 			}else if(a.equalsIgnoreCase("maf")){
jpayne@68: 				MAF_ins=MAF_noref=MAF_del=MAF_sub=Float.parseFloat(b);
jpayne@68: 			}else if(a.equalsIgnoreCase("mafindel")){
jpayne@68: 				MAF_ins=MAF_del=Float.parseFloat(b);
jpayne@68: 			}else if(a.equals("clearfilters")){
jpayne@68: 				if(Parse.parseBoolean(b)){
jpayne@68: 					samFilter.clear();
jpayne@68: 				}
jpayne@68: 			}else if(a.equals("parse_flag_goes_here")){
jpayne@68: 				long fake_variable=Parse.parseKMG(b);
jpayne@68: 				//Set a variable here
jpayne@68: 			}else if(samFilter.parse(arg, a, b)){
jpayne@68: 				//do nothing
jpayne@68: 			}else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
jpayne@68: 				//do nothing
jpayne@68: 			}else{
jpayne@68: 				outstream.println("Unknown parameter "+args[i]);
jpayne@68: 				assert(false) : "Unknown parameter "+args[i];
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(ref!=null && !Tools.existsInput(ref)){
jpayne@68: 			specialRef=ProkObject.isSpecialType(ref);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		return parser;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Add or remove .gz or .bz2 as needed */
jpayne@68: 	private void fixExtensions(){
jpayne@68: 		in=Tools.fixExtension(in);
jpayne@68: 		if(!specialRef){ref=Tools.fixExtension(ref);}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Ensure files can be read and written */
jpayne@68: 	private void checkFileExistence(){
jpayne@68: 
jpayne@68: 		//Ensure there is an input file
jpayne@68: 		if(in==null){throw new RuntimeException("Error - an input file is required.");}
jpayne@68: 
jpayne@68: 		//Ensure there is an input file
jpayne@68: 		if(ref==null){throw new RuntimeException("Error - a reference file is required.");}
jpayne@68: 		
jpayne@68: 		//Ensure output files can be written
jpayne@68: 		if(!Tools.testOutputFiles(overwrite, append, false, out, outModel, outHistFile)){
jpayne@68: 			outstream.println((out==null)+", "+out);
jpayne@68: 			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output file "+out+" or "+outModel+"\n");
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Ensure input files can be read
jpayne@68: 		if(!Tools.testInputFiles(true, true, in, inModelFile, (specialRef ? null : ref))){
jpayne@68: 			throw new RuntimeException("\nCan't read some input files.\n");  
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Ensure that no file was specified multiple times
jpayne@68: 		if(!Tools.testForDuplicateFiles(true, in, ref, out, outModel, outHistFile, inModelFile)){
jpayne@68: 			throw new RuntimeException("\nSome file names were specified multiple times.\n");
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Adjust file-related static fields as needed for this program */
jpayne@68: 	private static void checkStatics(){
jpayne@68: 		//Adjust the number of threads for input file reading
jpayne@68: 		if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
jpayne@68: 			ByteFile.FORCE_MODE_BF2=true;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		assert(FastaReadInputStream.settingsOK());
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Ensure parameter ranges are within bounds and required parameters are set */
jpayne@68: 	private boolean validateParams(){
jpayne@68: //		assert(minfoo>0 && minfoo<=maxfoo) : minfoo+", "+maxfoo;
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private void writeHist(String fname){
jpayne@68: 		ByteStreamWriter bsw=new ByteStreamWriter(fname, overwrite, append, false);
jpayne@68: 		bsw.start();
jpayne@68: 		bsw.print("#Value\tIdentity");
jpayne@68: 		if(inModel!=null){
jpayne@68: 			bsw.print("\tScore");
jpayne@68: 		}
jpayne@68: 		bsw.nl();
jpayne@68: 		for(int i=0; i<idHist.length; i++){
jpayne@68: 			bsw.print(0.01f*i, 2).tab().print(idHist[i]);
jpayne@68: 			if(inModel!=null){
jpayne@68: 				bsw.tab().print(scoreHist[i]);
jpayne@68: 			}
jpayne@68: 			bsw.nl();
jpayne@68: 		}
jpayne@68: 		errorState=bsw.poisonAndWait()|errorState;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Outer Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/** Create read streams and process all data */
jpayne@68: 	void process(Timer t){
jpayne@68: 		
jpayne@68: 		//Turn off read validation in the input threads to increase speed
jpayne@68: 		final boolean vic=Read.VALIDATE_IN_CONSTRUCTOR;
jpayne@68: 		Read.VALIDATE_IN_CONSTRUCTOR=Shared.threads()<4;
jpayne@68: 		
jpayne@68: 		//Load reference;
jpayne@68: 		refMap=loadReferenceCustom();
jpayne@68: 		makeRefMap2();
jpayne@68: 		
jpayne@68: 		//Reset counters
jpayne@68: 		readsProcessed=readsOut=0;
jpayne@68: 		basesProcessed=basesOut=0;
jpayne@68: 		alignedReads=0;
jpayne@68: 
jpayne@68: 		if(ffin.samOrBam()){
jpayne@68: 			//Create a read input stream
jpayne@68: 			final SamStreamer ss=makeStreamer(ffin);
jpayne@68: 			//Process the reads in separate threads
jpayne@68: 			spawnThreads(ss);
jpayne@68: 		}else{
jpayne@68: 			Shared.capBufferLen(40);
jpayne@68: 			//Create a read input stream
jpayne@68: 			final ConcurrentReadInputStream cris=makeCris(ffin);
jpayne@68: 			//Process the reads in separate threads
jpayne@68: 			spawnThreads(cris);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Optionally create a read output stream
jpayne@68: 		final ConcurrentReadOutputStream ros=makeCros();
jpayne@68: 		
jpayne@68: 		outputConsensus(ros);
jpayne@68: 		
jpayne@68: 		if(outHistFile!=null){
jpayne@68: 			writeHist(outHistFile);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(verbose){outstream.println("Finished; closing streams.");}
jpayne@68: 		
jpayne@68: 		//Write anything that was accumulated by ReadStats
jpayne@68: 		errorState|=ReadStats.writeAll();
jpayne@68: 		//Close the read streams
jpayne@68: 		errorState|=ReadWrite.closeStream(ros);
jpayne@68: 		
jpayne@68: 		//Reset read validation
jpayne@68: 		Read.VALIDATE_IN_CONSTRUCTOR=vic;
jpayne@68: 		
jpayne@68: 		//Report timing and results
jpayne@68: 		t.stop();
jpayne@68: 		if(!silent){
jpayne@68: 			outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
jpayne@68: 			outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false));
jpayne@68: 			outstream.println();
jpayne@68: 		}
jpayne@68: 		outstream.println(Tools.number("Ref Count:", refCount, 8));
jpayne@68: 		outstream.println(Tools.number("Sub Count:", subCount, 8));
jpayne@68: 		outstream.println(Tools.number("Del Count:", delCount, 8));
jpayne@68: 		outstream.println(Tools.number("Ins Count:", insCount, 8));
jpayne@68: 		outstream.println(Tools.number("Avg Identity:", 100*identitySum/alignedReads, 3, 8));
jpayne@68: 		if(scoreSum>0){
jpayne@68: 			outstream.println(Tools.number("Avg Score:", 100*scoreSum/alignedReads, 3, 8));
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Throw an exception of there was an error in a thread
jpayne@68: 		if(errorState){
jpayne@68: 			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	private synchronized LinkedHashMap<String, BaseGraph> loadReferenceCustom(){
jpayne@68: 		assert(!loadedRef);
jpayne@68: 		if(specialRef){return loadReferenceSpecial();}
jpayne@68: 		ConcurrentReadInputStream cris=makeRefCris();
jpayne@68: 		LinkedHashMap<String, BaseGraph> map=new LinkedHashMap<String, BaseGraph>();
jpayne@68: 		ListNum<Read> ln=cris.nextList();
jpayne@68: 		for(; ln!=null && !ln.isEmpty(); ln=cris.nextList()){
jpayne@68: 			if(verbose){outstream.println("Fetched "+ln.size()+" reference sequences.");}
jpayne@68: 			for(Read r : ln){
jpayne@68: 				if(r.bases!=null && r.bases.length>0){
jpayne@68: 					BaseGraph bg=new BaseGraph(r.id, r.bases, r.quality, r.numericID, 0);
jpayne@68: 					map.put(r.name(), bg);
jpayne@68: //					if(inModel!=null && inModel.name.equals(bg.name)){
jpayne@68: ////						assert(false) : Arrays.toString(bg.refWeights)+"\n"+Arrays.toString(inModel.refWeights);
jpayne@68: //						bg.refWeights=inModel.refWeights;
jpayne@68: //						bg.insWeights=inModel.insWeights;
jpayne@68: //						bg.delWeights=inModel.delWeights;
jpayne@68: //					}else{
jpayne@68: //						bg.insWeights=new float[bg.ref.length];
jpayne@68: //						bg.delWeights=new float[bg.ref.length];
jpayne@68: //						Arrays.fill(bg.insWeights, 1);
jpayne@68: //						Arrays.fill(bg.delWeights, 1);
jpayne@68: ////						assert(false) : Arrays.toString(bg.delWeights);
jpayne@68: //					}
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			if(ln!=null){
jpayne@68: 				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		if(verbose){outstream.println("Loaded "+map.size()+" reference sequences.");}
jpayne@68: 		loadedRef=true;
jpayne@68: 		return map;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	//For ribo subunits in resources directory
jpayne@68: 	private synchronized LinkedHashMap<String, BaseGraph> loadReferenceSpecial(){
jpayne@68: 		assert(!loadedRef);
jpayne@68: 		Read[] array=ProkObject.loadConsensusSequenceType(ref, false, false);
jpayne@68: 		Read r=array[0];
jpayne@68: 		BaseGraph bg=new BaseGraph(r.id, r.bases, r.quality, r.numericID, 0);
jpayne@68: 		LinkedHashMap<String, BaseGraph> map=new LinkedHashMap<String, BaseGraph>();
jpayne@68: 		map.put(r.name(), bg);
jpayne@68: 		return map;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	private synchronized void makeRefMap2(){
jpayne@68: 		assert(refMap!=null && refMap2==null);
jpayne@68: 		if(verbose){outstream.println("Making refMap2.");}
jpayne@68: 		refMap2=new LinkedHashMap<String, BaseGraph>((refMap.size()*3)/2);
jpayne@68: 		for(Entry<String, BaseGraph> e : refMap.entrySet()){
jpayne@68: 			String key=e.getKey();
jpayne@68: 			if(verbose){outstream.println("Considering "+key);}
jpayne@68: 			BaseGraph value=e.getValue();
jpayne@68: 			String key2=Tools.trimToWhitespace(key);
jpayne@68: 			if(verbose){outstream.println("key2="+key2);}
jpayne@68: //			if(verbose){outstream.println("put "+key2+", "+value);}
jpayne@68: 			refMap2.put(key2, value);
jpayne@68: //			if(verbose){outstream.println("putted "+key2+", "+value);}
jpayne@68: 			
jpayne@68: 			if(defaultRname==null){defaultRname=key;}
jpayne@68: 		}
jpayne@68: //		assert(false) : refMap+"\n"+refMap2;
jpayne@68: 		if(verbose){outstream.println("Made refMap2.");}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private ConcurrentReadInputStream makeRefCris(){
jpayne@68: 		ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffref, null);
jpayne@68: 		cris.start(); //Start the stream
jpayne@68: 		if(verbose){outstream.println("Started cris");}
jpayne@68: 		boolean paired=cris.paired();
jpayne@68: 		assert(!paired) : "References should not be paired.";
jpayne@68: 		return cris;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private SamStreamer makeStreamer(FileFormat ff){
jpayne@68: 		if(ff==null){return null;}
jpayne@68: 		SamStreamer ss=new SamReadStreamer(ff, streamerThreads, true, maxReads);
jpayne@68: 		ss.start(); //Start the stream
jpayne@68: 		if(verbose){outstream.println("Started Streamer");}
jpayne@68: 		return ss;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private ConcurrentReadInputStream makeCris(FileFormat ff){
jpayne@68: 		ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ff, null);
jpayne@68: 		cris.start(); //Start the stream
jpayne@68: 		if(verbose){outstream.println("Started cris");}
jpayne@68: 		boolean paired=cris.paired();
jpayne@68: 		assert(!paired);
jpayne@68: 		return cris;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private ConcurrentReadOutputStream makeCros(){
jpayne@68: 		if(ffout==null){return null;}
jpayne@68: 
jpayne@68: 		//Select output buffer size based on whether it needs to be ordered
jpayne@68: 		final int buff=(ordered ? Tools.mid(16, 128, (Shared.threads()*2)/3) : 8);
jpayne@68: 		
jpayne@68: 		final ConcurrentReadOutputStream ros=ConcurrentReadOutputStream.getStream(ffout, null, buff, null, false);
jpayne@68: 		ros.start(); //Start the stream
jpayne@68: 		return ros;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------       Thread Management      ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** Spawn process threads */
jpayne@68: 	private void spawnThreads(final SamStreamer ss){
jpayne@68: 		
jpayne@68: 		//Do anything necessary prior to processing
jpayne@68: 		
jpayne@68: 		//Determine how many threads may be used
jpayne@68: 		final int threads=Shared.threads();
jpayne@68: 		
jpayne@68: 		//Fill a list with ProcessThreads
jpayne@68: 		ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
jpayne@68: 		for(int i=0; i<threads; i++){
jpayne@68: 			alpt.add(new ProcessThread(ss, i));
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Start the threads
jpayne@68: 		for(ProcessThread pt : alpt){
jpayne@68: 			pt.start();
jpayne@68: 		}
jpayne@68: 		if(verbose){outstream.println("Started worker threads.");}
jpayne@68: 		
jpayne@68: 		//Wait for threads to finish
jpayne@68: 		boolean success=ThreadWaiter.waitForThreads(alpt, this);
jpayne@68: 		errorState&=!success;
jpayne@68: 		
jpayne@68: 		//Do anything necessary after processing
jpayne@68: 		
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Spawn process threads */
jpayne@68: 	private void spawnThreads(final ConcurrentReadInputStream cris){
jpayne@68: 		
jpayne@68: 		//Do anything necessary prior to processing
jpayne@68: 		
jpayne@68: 		//Determine how many threads may be used
jpayne@68: 		final int threads=Shared.threads();
jpayne@68: 		
jpayne@68: 		//Fill a list with ProcessThreads
jpayne@68: 		ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
jpayne@68: 		for(int i=0; i<threads; i++){
jpayne@68: 			alpt.add(new ProcessThread(cris, i));
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Start the threads
jpayne@68: 		for(ProcessThread pt : alpt){
jpayne@68: 			pt.start();
jpayne@68: 		}
jpayne@68: 		if(verbose){outstream.println("Started worker threads.");}
jpayne@68: 		
jpayne@68: 		//Wait for threads to finish
jpayne@68: 		boolean success=ThreadWaiter.waitForThreads(alpt, this);
jpayne@68: 		errorState&=!success;
jpayne@68: 		
jpayne@68: 		//Do anything necessary after processing
jpayne@68: 		ReadWrite.closeStreams(cris);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private void outputConsensus(ConcurrentReadOutputStream ros){
jpayne@68: 		if(verbose){outstream.println("Making consensus.");}
jpayne@68: 		ArrayList<Read> consensusList=new ArrayList<Read>(200);
jpayne@68: 		ArrayList<BaseGraph> graphList=new ArrayList<BaseGraph>(200);
jpayne@68: 		long num=0;
jpayne@68: 		for(Entry<String, BaseGraph> e : refMap.entrySet()){
jpayne@68: 			BaseGraph bg=e.getValue();
jpayne@68: 			graphList.add(bg);
jpayne@68: 			
jpayne@68: 			Read r=bg.traverse();
jpayne@68: 			if(name!=null){r.id=name;}
jpayne@68: 			consensusList.add(r);
jpayne@68: 			
jpayne@68: 			refCount+=bg.refCount;
jpayne@68: 			subCount+=bg.subCount;
jpayne@68: 			delCount+=bg.delCount;
jpayne@68: 			insCount+=bg.insCount;
jpayne@68: 			
jpayne@68: 			readsOut++;
jpayne@68: 			basesOut+=r.length();
jpayne@68: 			
jpayne@68: 			if(consensusList.size()>=200){
jpayne@68: 				if(ros!=null){ros.add(consensusList, num);}
jpayne@68: 				consensusList=new ArrayList<Read>(200);
jpayne@68: 				num++;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		if(consensusList.size()>0){
jpayne@68: 			if(ros!=null){ros.add(consensusList, num);}
jpayne@68: 			consensusList=new ArrayList<Read>(200);
jpayne@68: 			num++;
jpayne@68: 		}
jpayne@68: 		if(graphList.size()>0 && ffmodel!=null){
jpayne@68: //			ReadWrite.writeObjectInThread(graphList, ffmodel.name(), true);
jpayne@68: 			ReadWrite.writeAsync(graphList, ffmodel.name(), true);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final void accumulate(ProcessThread pt){
jpayne@68: 		readsProcessed+=pt.readsProcessedT;
jpayne@68: 		basesProcessed+=pt.basesProcessedT;
jpayne@68: 		alignedReads+=pt.alignedReadsT;
jpayne@68: 		identitySum+=pt.identitySumT;
jpayne@68: 		scoreSum+=pt.scoreSumT;
jpayne@68: 		for(int i=0; i<idHist.length; i++){
jpayne@68: 			idHist[i]+=pt.idHistT[i];
jpayne@68: 			scoreHist[i]+=pt.scoreHistT[i];
jpayne@68: 		}
jpayne@68: 		errorState|=(!pt.success);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final boolean success(){return !errorState;}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Inner Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public ByteBuilder toText() {
jpayne@68: 		// TODO Auto-generated method stub
jpayne@68: 		return null;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Inner Classes        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** This class is static to prevent accidental writing to shared variables.
jpayne@68: 	 * It is safe to remove the static modifier. */
jpayne@68: 	class ProcessThread extends Thread {
jpayne@68: 		
jpayne@68: 		//Constructor
jpayne@68: 		ProcessThread(final SamStreamer ss_, final int tid_){
jpayne@68: 			ss=ss_;
jpayne@68: 			cris=null;
jpayne@68: 			tid=tid_;
jpayne@68: 			realigner=(realign ? new Realigner() : null);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Constructor
jpayne@68: 		ProcessThread(final ConcurrentReadInputStream cris_, final int tid_){
jpayne@68: 			ss=null;
jpayne@68: 			cris=cris_;
jpayne@68: 			tid=tid_;
jpayne@68: 			realigner=null;//(realign ? new Realigner() : null);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Called by start()
jpayne@68: 		@Override
jpayne@68: 		public void run(){
jpayne@68: 			//Do anything necessary prior to processing
jpayne@68: 			
jpayne@68: 			//Process the reads
jpayne@68: 			processInner();
jpayne@68: 			
jpayne@68: 			//Do anything necessary after processing
jpayne@68: 			
jpayne@68: 			//Indicate successful exit status
jpayne@68: 			success=true;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		/** Iterate through the reads */
jpayne@68: 		void processInner(){
jpayne@68: 			
jpayne@68: 			
jpayne@68: 			//Grab and process all lists
jpayne@68: 			
jpayne@68: 			if(ss!=null){
jpayne@68: 				for(ListNum<Read> ln=ss.nextReads(); ln!=null; ln=ss.nextReads()){
jpayne@68: 					processList(ln);
jpayne@68: 				}
jpayne@68: 			}else{
jpayne@68: 				for(ListNum<Read> ln=cris.nextList(); ln!=null && ln.size()>0; ln=cris.nextList()){
jpayne@68: 					processList(ln);
jpayne@68: 					cris.returnList(ln);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		void processList(ListNum<Read> ln){
jpayne@68: 			
jpayne@68: 			//Loop through each read in the list
jpayne@68: 			for(Read r : ln){
jpayne@68: 				
jpayne@68: 				//Validate reads in worker threads
jpayne@68: 				if(!r.validated()){r.validate(true);}
jpayne@68: 
jpayne@68: 				//Track the initial length for statistics
jpayne@68: 				final int initialLength=r.length();
jpayne@68: 
jpayne@68: 				//Increment counters
jpayne@68: 				readsProcessedT++;
jpayne@68: 				basesProcessedT+=initialLength;
jpayne@68: 				
jpayne@68: 				{
jpayne@68: 					//Reads are processed in this block.
jpayne@68: 					processRead(r);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		/**
jpayne@68: 		 * Process a read or a read pair.
jpayne@68: 		 * @param r Read 1
jpayne@68: 		 * @param r2 Read 2 (may be null)
jpayne@68: 		 * @return True if the reads should be kept, false if they should be discarded.
jpayne@68: 		 */
jpayne@68: 		void processRead(final Read r){
jpayne@68: 			if(r.bases==null || r.length()<=1){return;}
jpayne@68: 			
jpayne@68: 			final SamLine sl=r.samline;
jpayne@68: 			if(sl!=null && !sl.mapped()){return;}
jpayne@68: 			final String rname=(sl==null ? defaultRname : sl.rnameS());
jpayne@68: 			BaseGraph bg=refMap.get(rname);
jpayne@68: 			if(bg==null){bg=refMap2.get(Tools.trimToWhitespace(rname));}
jpayne@68: 			assert(bg!=null) : "Can't find graph for "+rname;
jpayne@68: 			float identity;
jpayne@68: 			float score=0;//unused
jpayne@68: 
jpayne@68: //			assert(false) : r;
jpayne@68: 			if(sl==null){
jpayne@68: //				identity=SketchObject.alignAndMakeMatch(r, bg.original);
jpayne@68: //				assert(false) : bg.refWeights[0];
jpayne@68: //				identity=SketchObject.alignAndMakeMatch(r, bg.original, bg.refWeights, bg.insWeights, bg.delWeights);
jpayne@68: 				identity=SketchObject.alignAndMakeMatch(r, bg.original, bg.refWeights);
jpayne@68: 				if(identity<=0){return;}
jpayne@68: 				assert(r.match!=null) : identity+", "+r;
jpayne@68: 			}else{
jpayne@68: 				assert(sl!=null && sl.mapped() && sl.seq!=null) : sl;
jpayne@68: 				assert(r.match!=null);
jpayne@68: 				if(samFilter!=null && !samFilter.passesFilter(sl)){return;}
jpayne@68: 				identity=sl.calcIdentity();
jpayne@68: 			}
jpayne@68: 			assert(r.match!=null && identity>0) : identity+", "+r;
jpayne@68: 			
jpayne@68: 			if(inModel!=null){
jpayne@68: 
jpayne@68: 				if(verbose){System.err.println(r.start+"\t"+r.stop+"\t"+new String(r.match));}
jpayne@68: 				score=inModel.score(r, false, true);
jpayne@68: 				if(printScores){
jpayne@68: //					System.err.println(identity+"\t"+score+"\t"+inModel.score(r, false, true));
jpayne@68: 					System.err.println(String.format("%.5f\t%.5f", identity, score));
jpayne@68: 				}
jpayne@68: //				assert(false);
jpayne@68: //				if(score<0){
jpayne@68: //					verbose=true;
jpayne@68: //					inModel.score(r, false, false);
jpayne@68: //				}
jpayne@68: //				assert(!verbose);
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			alignedReadsT++;
jpayne@68: 			identitySumT+=identity;
jpayne@68: 			scoreSumT+=score;
jpayne@68: 			idHistT[Tools.mid(0, Math.round(100*identity), 100)]++;
jpayne@68: 			scoreHistT[Tools.mid(0, Math.round(100*score), 100)]++;
jpayne@68: 			
jpayne@68: 			
jpayne@68: 			
jpayne@68: //			assert(sl.calcIdentity()<=0.78) : sl.calcIdentity()+", "+samFilter.maxId;
jpayne@68: //			assert(false) : sl.cigar+", "+sl.calcIdentity();
jpayne@68: 			
jpayne@68: //			System.err.println(rname);
jpayne@68: 			
jpayne@68: 			if(realigner!=null) {
jpayne@68: 				assert(false);
jpayne@68: 				realigner.realign(r, sl, bg.original, true);
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			bg.add(r);
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		long[] idHistT=new long[101];
jpayne@68: 		long[] scoreHistT=new long[101];
jpayne@68: 
jpayne@68: 		/** Number of reads processed by this thread */
jpayne@68: 		protected long readsProcessedT=0;
jpayne@68: 		/** Number of bases processed by this thread */
jpayne@68: 		protected long basesProcessedT=0;
jpayne@68: 		
jpayne@68: 		protected long alignedReadsT=0;
jpayne@68: 
jpayne@68: 		double identitySumT=0;
jpayne@68: 		double scoreSumT=0;
jpayne@68: 		
jpayne@68: 		/** True only if this thread has completed successfully */
jpayne@68: 		boolean success=false;
jpayne@68: 
jpayne@68: 		/** Shared input stream */
jpayne@68: 		private final SamStreamer ss;
jpayne@68: 		/** Alternate input stream */
jpayne@68: 		private final ConcurrentReadInputStream cris;
jpayne@68: 		/** Thread ID */
jpayne@68: 		final int tid;
jpayne@68: 		/** For realigning reads */
jpayne@68: 		final Realigner realigner;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/** Read input file path */
jpayne@68: 	private String in=null;
jpayne@68: 	/** Reference input file path */
jpayne@68: 	private String ref=null;
jpayne@68: 
jpayne@68: 	private String inModelFile;
jpayne@68: 	private BaseGraph inModel;
jpayne@68: 	private String outHistFile;
jpayne@68: 	
jpayne@68: 	/** Consensus output file path */
jpayne@68: 	private String out=null;
jpayne@68: 	/** Model output file path */
jpayne@68: 	private String outModel=null;
jpayne@68: 	
jpayne@68: 	/** Override input file extension */
jpayne@68: 	private String extin=null;
jpayne@68: 	/** Override output file extension */
jpayne@68: 	private String extout=null;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/** Number of reads processed */
jpayne@68: 	protected long readsProcessed=0;
jpayne@68: 	/** Number of bases processed */
jpayne@68: 	protected long basesProcessed=0;
jpayne@68: 	
jpayne@68: 	protected long alignedReads=0;
jpayne@68: 
jpayne@68: 	protected double identitySum=0;
jpayne@68: 	protected double scoreSum=0;
jpayne@68: 
jpayne@68: 	/** Number of reads retained */
jpayne@68: 	protected long readsOut=0;
jpayne@68: 	/** Number of bases retained */
jpayne@68: 	protected long basesOut=0;
jpayne@68: 
jpayne@68: 	/** Quit after processing this many input reads; -1 means no limit */
jpayne@68: 	private long maxReads=-1;
jpayne@68: 	
jpayne@68: 	public long subCount=0;
jpayne@68: 	public long refCount=0;
jpayne@68: 	public long delCount=0;
jpayne@68: 	public long insCount=0;
jpayne@68: 
jpayne@68: 	long[] idHist=new long[101];
jpayne@68: 	long[] scoreHist=new long[101];
jpayne@68: 	boolean printScores=false;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** Threads dedicated to reading the sam file */
jpayne@68: 	private int streamerThreads=SamStreamer.DEFAULT_THREADS;
jpayne@68: 	
jpayne@68: 	private String name=null;
jpayne@68: 
jpayne@68: 	private boolean loadedRef=false;
jpayne@68: 	private boolean specialRef=false;
jpayne@68: 	
jpayne@68: 	private boolean realign=false;
jpayne@68: 	
jpayne@68: 	private int ploidy=1;
jpayne@68: 	
jpayne@68: 	private final boolean silent;
jpayne@68: 	
jpayne@68: 	public final SamFilter samFilter=new SamFilter();
jpayne@68: 	/** Uses full ref names */
jpayne@68: 	public LinkedHashMap<String, BaseGraph> refMap;
jpayne@68: 	/** Uses truncated ref names */
jpayne@68: 	public LinkedHashMap<String, BaseGraph> refMap2;
jpayne@68: 	
jpayne@68: 	private String defaultRname=null;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Final Fields         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** Read input file */
jpayne@68: 	private final FileFormat ffin;
jpayne@68: 	/** Reference input file */
jpayne@68: 	private final FileFormat ffref;
jpayne@68: 
jpayne@68: 	/** Consensus output file */
jpayne@68: 	private final FileFormat ffout;
jpayne@68: 	/** Model output file */
jpayne@68: 	private final FileFormat ffmodel;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Common Fields         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** Print status messages to this output stream */
jpayne@68: 	private PrintStream outstream=System.err;
jpayne@68: 	/** True if an error was encountered */
jpayne@68: 	public boolean errorState=false;
jpayne@68: 	/** Overwrite existing output files */
jpayne@68: 	private boolean overwrite=false;
jpayne@68: 	/** Append to existing output files */
jpayne@68: 	private boolean append=false;
jpayne@68: 	/** Reads ARE output in input order, even though this is false */
jpayne@68: 	private final boolean ordered=false;
jpayne@68: 	
jpayne@68: }