jpayne@68: package prok;
jpayne@68: 
jpayne@68: import java.io.File;
jpayne@68: import java.io.PrintStream;
jpayne@68: import java.util.ArrayList;
jpayne@68: import java.util.PriorityQueue;
jpayne@68: 
jpayne@68: import aligner.Alignment;
jpayne@68: import dna.AminoAcid;
jpayne@68: import fileIO.ByteFile;
jpayne@68: import fileIO.FileFormat;
jpayne@68: import fileIO.ReadWrite;
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 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.ReadInputStream;
jpayne@68: import structures.ListNum;
jpayne@68: import structures.LongHashSet;
jpayne@68: import template.Accumulator;
jpayne@68: import template.ThreadWaiter;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * Makes a consensus ribosomal sequence using raw reads as input.
jpayne@68:  * 
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date October 10, 2019
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class RiboMaker implements Accumulator<RiboMaker.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: 		assert(false) : "TODO";
jpayne@68: 		
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: 		RiboMaker x=new RiboMaker(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 RiboMaker(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: 		
jpayne@68: 		{//Parse the arguments
jpayne@68: 			final Parser parser=parse(args);
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: 			setInterleaved=parser.setInterleaved;
jpayne@68: 			
jpayne@68: 			in1=parser.in1;
jpayne@68: 			in2=parser.in2;
jpayne@68: 			qfin1=parser.qfin1;
jpayne@68: 			qfin2=parser.qfin2;
jpayne@68: 			extin=parser.extin;
jpayne@68: 
jpayne@68: 			out1=parser.out1;
jpayne@68: 			qfout1=parser.qfout1;
jpayne@68: 			extout=parser.extout;
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		validateParams();
jpayne@68: 		doPoundReplacement(); //Replace # with 1 and 2
jpayne@68: 		adjustInterleaving(); //Make sure interleaving agrees with number of input and output files
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: 		ffout1=FileFormat.testOutput(out1, FileFormat.FASTQ, extout, true, overwrite, append, ordered);
jpayne@68: 		
jpayne@68: 		fffilter=FileFormat.testInput(filterFile, FileFormat.FASTA, null, true, true);
jpayne@68: 		ffref=FileFormat.testInput(refFile, FileFormat.FASTA, null, true, true);
jpayne@68: 
jpayne@68: 		//Create input FileFormat objects
jpayne@68: 		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
jpayne@68: 		ffin2=FileFormat.testInput(in2, FileFormat.FASTQ, extin, true, true);
jpayne@68: 		
jpayne@68: 		if(fffilter==null){
jpayne@68: 			filter=null;
jpayne@68: 		}else{
jpayne@68: 			filter=loadFilter(fffilter, k);
jpayne@68: 		}
jpayne@68: 		loadRef();
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: 			}else if(a.equals("ordered")){
jpayne@68: 				ordered=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("filter")){
jpayne@68: 				filterFile=b;
jpayne@68: 			}else if(a.equals("ref")){
jpayne@68: 				refFile=b;
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(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: 		return parser;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Replace # with 1 and 2 in headers */
jpayne@68: 	private void doPoundReplacement(){
jpayne@68: 		//Do input file # replacement
jpayne@68: 		if(in1!=null && in2==null && in1.indexOf('#')>-1 && !new File(in1).exists()){
jpayne@68: 			in2=in1.replace("#", "2");
jpayne@68: 			in1=in1.replace("#", "1");
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Ensure there is an input file
jpayne@68: 		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Add or remove .gz or .bz2 as needed */
jpayne@68: 	private void fixExtensions(){
jpayne@68: 		in1=Tools.fixExtension(in1);
jpayne@68: 		in2=Tools.fixExtension(in2);
jpayne@68: 		qfin1=Tools.fixExtension(qfin1);
jpayne@68: 		qfin2=Tools.fixExtension(qfin2);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Ensure files can be read and written */
jpayne@68: 	private void checkFileExistence(){
jpayne@68: 		//Ensure output files can be written
jpayne@68: 		if(!Tools.testOutputFiles(overwrite, append, false, out1)){
jpayne@68: 			outstream.println((out1==null)+", "+out1);
jpayne@68: 			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+"\n");
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Ensure input files can be read
jpayne@68: 		if(!Tools.testInputFiles(false, true, in1, in2, filterFile, refFile)){
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, in1, in2, out1, filterFile, refFile)){
jpayne@68: 			throw new RuntimeException("\nSome file names were specified multiple times.\n");
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		assert(refFile!=null);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Make sure interleaving agrees with number of input and output files */
jpayne@68: 	private void adjustInterleaving(){
jpayne@68: 		//Adjust interleaved detection based on the number of input files
jpayne@68: 		if(in2!=null){
jpayne@68: 			if(FASTQ.FORCE_INTERLEAVED){outstream.println("Reset INTERLEAVED to false because paired input files were specified.");}
jpayne@68: 			FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		//Adjust interleaved settings based on number of output files
jpayne@68: 		if(!setInterleaved){
jpayne@68: 			assert(in1!=null) : "\nin1="+in1+"\nin2="+in2+"\nout1="+out1+"\n";
jpayne@68: 			if(in2!=null){ //If there are 2 input streams.
jpayne@68: 				FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
jpayne@68: 				outstream.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
jpayne@68: 			}
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: 		assert(false) : "TODO";
jpayne@68: 		return true;
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: 		//Create a read input stream
jpayne@68: 		final ConcurrentReadInputStream cris=makeCris();
jpayne@68: 		
jpayne@68: 		//Optionally create a read output stream
jpayne@68: 		final ConcurrentReadOutputStream ros=makeCros(cris.paired());
jpayne@68: 		
jpayne@68: 		//Reset counters
jpayne@68: 		readsProcessed=readsOut=0;
jpayne@68: 		basesProcessed=basesOut=0;
jpayne@68: 		
jpayne@68: 		//Process the reads in separate threads
jpayne@68: 		spawnThreads(cris, ros);
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.closeStreams(cris, 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: 		outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
jpayne@68: 		outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false));
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 void loadRef(){
jpayne@68: 		ArrayList<Read> reads=ReadInputStream.toReads(ffref, -1);
jpayne@68: 		ref0=reads.get(0).bases;
jpayne@68: 		ref=new byte[ref0.length+2*padding];
jpayne@68: 		for(int i=0, j=-padding; i<ref.length; i++, j++){
jpayne@68: 			byte b=(j>=0 && j<ref0.length ? ref0[j] : (byte)'N');
jpayne@68: 			ref[i]=b;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		queues=new PriorityQueue[1+ref.length/queueWidth];
jpayne@68: 		for(int i=0; i<queues.length; i++){
jpayne@68: 			queues[i]=new PriorityQueue<Alignment>(queueLen);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static LongHashSet loadFilter(FileFormat ff, int k){
jpayne@68: 		if(ff==null){return null;}
jpayne@68: 		ArrayList<Read> reads=ReadInputStream.toReads(ff, -1);
jpayne@68: 		if(reads==null || reads.size()==0){return null;}
jpayne@68: 		LongHashSet set=new LongHashSet(4096);
jpayne@68: 
jpayne@68: 		final int shift=2*k;
jpayne@68: 		final int shift2=shift-2;
jpayne@68: 		final long mask=(shift>63 ? -1L : ~((-1L)<<shift));
jpayne@68: 		int len=0;
jpayne@68: 		
jpayne@68: 		long kmer=0, rkmer=0;
jpayne@68: 		for(Read r : reads){
jpayne@68: 			final byte[] bases=r.bases;
jpayne@68: 			for(byte b : bases) {
jpayne@68: 				long x=AminoAcid.baseToNumber[b];
jpayne@68: 				long x2=AminoAcid.baseToComplementNumber[b];
jpayne@68: 				kmer=((kmer<<2)|x)&mask;
jpayne@68: 				rkmer=((rkmer>>>2)|(x2<<shift2))&mask;
jpayne@68: 				
jpayne@68: 				if(x>=0){
jpayne@68: 					len++;
jpayne@68: 					if(len>=k){
jpayne@68: 						set.add(Tools.max(kmer, rkmer));
jpayne@68: 					}
jpayne@68: 				}else{
jpayne@68: 					len=0;
jpayne@68: 					kmer=rkmer=0;
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return set;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static boolean passesFilter(Read r, int k, LongHashSet set){
jpayne@68: 		if(r==null) {return false;}
jpayne@68: 		if(set==null){return true;}
jpayne@68: 
jpayne@68: 		final int shift=2*k;
jpayne@68: 		final int shift2=shift-2;
jpayne@68: 		final long mask=(shift>63 ? -1L : ~((-1L)<<shift));
jpayne@68: 		int len=0;
jpayne@68: 		long kmer=0, rkmer=0;
jpayne@68: 
jpayne@68: 		final byte[] bases=r.bases;
jpayne@68: 		for(byte b : bases) {
jpayne@68: 			long x=AminoAcid.baseToNumber[b];
jpayne@68: 			long x2=AminoAcid.baseToComplementNumber[b];
jpayne@68: 			kmer=((kmer<<2)|x)&mask;
jpayne@68: 			rkmer=((rkmer>>>2)|(x2<<shift2))&mask;
jpayne@68: 
jpayne@68: 			if(x>=0){
jpayne@68: 				len++;
jpayne@68: 				if(len>=k){
jpayne@68: 					long key=Tools.max(kmer, rkmer);
jpayne@68: 					if(set.contains(key)){return true;}
jpayne@68: 				}
jpayne@68: 			}else{
jpayne@68: 				len=0;
jpayne@68: 				kmer=rkmer=0;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return false;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private ConcurrentReadInputStream makeCris(){
jpayne@68: 		ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
jpayne@68: 		cris.start(); //Start the stream
jpayne@68: 		if(verbose){outstream.println("Started cris");}
jpayne@68: 		boolean paired=cris.paired();
jpayne@68: 		if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
jpayne@68: 		return cris;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private ConcurrentReadOutputStream makeCros(boolean pairedInput){
jpayne@68: 		if(ffout1==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(ffout1, null, qfout1, 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 ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros){
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 and wait for them to finish
jpayne@68: 		boolean success=ThreadWaiter.startAndWait(alpt, this);
jpayne@68: 		errorState&=!success;
jpayne@68: 		
jpayne@68: 		//Do anything necessary after processing
jpayne@68: 		assert(false) : "TODO: Make consensus and write it?";
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: 		readsOut+=pt.readsOutT;
jpayne@68: 		basesOut+=pt.basesOutT;
jpayne@68: 		errorState|=(!pt.success);
jpayne@68: 
jpayne@68: 		for(int i=0; i<queues.length; i++){
jpayne@68: 			PriorityQueue<Alignment> q=queues[i];
jpayne@68: 			PriorityQueue<Alignment> qt=pt.queuesT[i];
jpayne@68: 			for(Alignment a : qt){
jpayne@68: 				addToQueue(a, q);
jpayne@68: 			}
jpayne@68: 		}
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: 	boolean addToQueue(Alignment best, PriorityQueue<Alignment>[] queues){
jpayne@68: 		int start=best.start;
jpayne@68: 		int qnum=start/queueWidth;
jpayne@68: 		PriorityQueue<Alignment> queue=queues[qnum];
jpayne@68: 		return addToQueue(best, queue);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	boolean addToQueue(Alignment best, PriorityQueue<Alignment> queue){
jpayne@68: 		if(queue.size()<queueLen){queue.add(best);}
jpayne@68: 		else{
jpayne@68: 			Alignment bottom=queue.peek();
jpayne@68: 			if(bottom.compareTo(best)>=0){return false;}
jpayne@68: 			queue.poll();
jpayne@68: 			queue.add(best);
jpayne@68: 		}
jpayne@68: 		return true;
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 ConcurrentReadInputStream cris_, final int tid_){
jpayne@68: 			cris=cris_;
jpayne@68: 			tid=tid_;
jpayne@68: 			
jpayne@68: 			queuesT=new PriorityQueue[1+ref.length/queueWidth];
jpayne@68: 			for(int i=0; i<queuesT.length; i++){
jpayne@68: 				queuesT[i]=new PriorityQueue<Alignment>(queueLen);
jpayne@68: 			}
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: 			//Grab the first ListNum of reads
jpayne@68: 			ListNum<Read> ln=cris.nextList();
jpayne@68: 
jpayne@68: 			//Check to ensure pairing is as expected
jpayne@68: 			if(ln!=null && !ln.isEmpty()){
jpayne@68: 				Read r=ln.get(0);
jpayne@68: //				assert(ffin1.samOrBam() || (r.mate!=null)==cris.paired()); //Disabled due to non-static access
jpayne@68: 			}
jpayne@68: 
jpayne@68: 			//As long as there is a nonempty read list...
jpayne@68: 			while(ln!=null && ln.size()>0){
jpayne@68: //				if(verbose){outstream.println("Fetched "+reads.size()+" reads.");} //Disabled due to non-static access
jpayne@68: 				
jpayne@68: 				processList(ln);
jpayne@68: 				
jpayne@68: 				//Notify the input stream that the list was used
jpayne@68: 				cris.returnList(ln);
jpayne@68: //				if(verbose){outstream.println("Returned a list.");} //Disabled due to non-static access
jpayne@68: 				
jpayne@68: 				//Fetch a new list
jpayne@68: 				ln=cris.nextList();
jpayne@68: 			}
jpayne@68: 
jpayne@68: 			//Notify the input stream that the final list was used
jpayne@68: 			if(ln!=null){
jpayne@68: 				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		void processList(ListNum<Read> ln){
jpayne@68: 
jpayne@68: 			//Grab the actual read list from the ListNum
jpayne@68: 			final ArrayList<Read> reads=ln.list;
jpayne@68: 			
jpayne@68: 			//Loop through each read in the list
jpayne@68: 			for(int idx=0; idx<reads.size(); idx++){
jpayne@68: 				final Read r1=reads.get(idx);
jpayne@68: 				final Read r2=r1.mate;
jpayne@68: 				
jpayne@68: 				//Validate reads in worker threads
jpayne@68: 				if(!r1.validated()){r1.validate(true);}
jpayne@68: 				if(r2!=null && !r2.validated()){r2.validate(true);}
jpayne@68: 
jpayne@68: 				//Track the initial length for statistics
jpayne@68: 				final int initialLength1=r1.length();
jpayne@68: 				final int initialLength2=r1.mateLength();
jpayne@68: 
jpayne@68: 				//Increment counters
jpayne@68: 				readsProcessedT+=r1.pairCount();
jpayne@68: 				basesProcessedT+=initialLength1+initialLength2;
jpayne@68: 				
jpayne@68: 				{
jpayne@68: 					//Reads are processed in this block.
jpayne@68: 					processReadPair(r1, r2);
jpayne@68: 					
jpayne@68: //					if(!keep){reads.set(idx, null);}
jpayne@68: //					else{
jpayne@68: //						readsOutT+=r1.pairCount();
jpayne@68: //						basesOutT+=r1.pairLength();
jpayne@68: //					}
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 
jpayne@68: 			//Output reads to the output stream
jpayne@68: //			if(ros!=null){ros.add(reads, ln.id);}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		/**
jpayne@68: 		 * Process a read or a read pair.
jpayne@68: 		 * @param r1 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 processReadPair(final Read r1, final Read r2){
jpayne@68: 			boolean pass=passesFilter(r1, k, filter) || passesFilter(r2, k, filter);
jpayne@68: 			if(!pass){return;}
jpayne@68: 			processRead(r1);
jpayne@68: 			processRead(r2);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		void processRead(final Read r){
jpayne@68: 			Alignment plus=new Alignment(r);
jpayne@68: 			plus.align(ref);
jpayne@68: 			
jpayne@68: 			r.reverseComplement();
jpayne@68: 			Alignment minus=new Alignment(r);
jpayne@68: 			minus.align(ref);
jpayne@68: 			
jpayne@68: 			Alignment best=null;
jpayne@68: 			if(plus.id>=minus.id){
jpayne@68: 				r.reverseComplement();
jpayne@68: 				best=plus;
jpayne@68: 			}else{
jpayne@68: 				best=minus;
jpayne@68: 			}
jpayne@68: 			if(best.id<minID) {return;}
jpayne@68: 			
jpayne@68: 			addToQueue(best, queuesT);
jpayne@68: 		}
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: 		/** Number of reads retained by this thread */
jpayne@68: 		protected long readsOutT=0;
jpayne@68: 		/** Number of bases retained by this thread */
jpayne@68: 		protected long basesOutT=0;
jpayne@68: 		
jpayne@68: 		/** True only if this thread has completed successfully */
jpayne@68: 		boolean success=false;
jpayne@68: 		
jpayne@68: 
jpayne@68: 		private PriorityQueue<Alignment>[] queuesT;
jpayne@68: 		
jpayne@68: 		/** Shared input stream */
jpayne@68: 		private final ConcurrentReadInputStream cris;
jpayne@68: 		/** Thread ID */
jpayne@68: 		final int tid;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/** Primary input file path */
jpayne@68: 	private String in1=null;
jpayne@68: 	/** Secondary input file path */
jpayne@68: 	private String in2=null;
jpayne@68: 	
jpayne@68: 	private String qfin1=null;
jpayne@68: 	private String qfin2=null;
jpayne@68: 
jpayne@68: 	/** Primary output file path */
jpayne@68: 	private String out1=null;
jpayne@68: 
jpayne@68: 	private String qfout1=null;
jpayne@68: 	
jpayne@68: 	private String filterFile;
jpayne@68: 	private String refFile;
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: 	/** Whether interleaved was explicitly set. */
jpayne@68: 	private boolean setInterleaved=false;
jpayne@68: 
jpayne@68: 	/** Original ref */
jpayne@68: 	private byte[] ref0;
jpayne@68: 	/** Padded ref */
jpayne@68: 	private byte[] ref;
jpayne@68: 	
jpayne@68: 	private int padding=100;
jpayne@68: 	private int queueLen=20;
jpayne@68: 	private int queueWidth=20;
jpayne@68: 	private float minID=0.4f;
jpayne@68: 	
jpayne@68: 	private PriorityQueue<Alignment>[] queues;
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: 	/** 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: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Final Fields         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/** Primary input file */
jpayne@68: 	private final FileFormat ffin1;
jpayne@68: 	/** Secondary input file */
jpayne@68: 	private final FileFormat ffin2;
jpayne@68: 	/** Filter input file */
jpayne@68: 	private final FileFormat fffilter;
jpayne@68: 	/** Ref input file */
jpayne@68: 	private final FileFormat ffref;
jpayne@68: 	
jpayne@68: 	/** Primary output file */
jpayne@68: 	private final FileFormat ffout1;
jpayne@68: 	
jpayne@68: 	private final LongHashSet filter;
jpayne@68: 	private final int k=31;
jpayne@68: 	
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: 	/** Print verbose messages */
jpayne@68: 	public static boolean verbose=false;
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 */
jpayne@68: 	private boolean ordered=false;
jpayne@68: 	
jpayne@68: }