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.Collections;
jpayne@68: import java.util.Comparator;
jpayne@68: import java.util.HashMap;
jpayne@68: import java.util.Map.Entry;
jpayne@68: import java.util.concurrent.ConcurrentLinkedQueue;
jpayne@68: 
jpayne@68: import aligner.SingleStateAlignerFlat2;
jpayne@68: import consensus.BaseGraph;
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 structures.IntHashSet;
jpayne@68: import structures.ListNum;
jpayne@68: import tax.GiToTaxid;
jpayne@68: import template.Accumulator;
jpayne@68: import template.ThreadWaiter;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * Picks one ribosomal (16S) sequence per taxID.
jpayne@68:  * 
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date November 19, 2015
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class MergeRibo implements Accumulator<MergeRibo.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: 		MergeRibo x=new MergeRibo(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 MergeRibo(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: //		Shared.capBufferLen(40);//This does not help; the slowness comes from unevenness in list length during pickBest.
jpayne@68: 		//To fix it, long lists should be sorted to be first.
jpayne@68: 		
jpayne@68: 		BaseGraph.MAF_sub=0.251f;
jpayne@68: 		BaseGraph.MAF_del=0.0f;
jpayne@68: 		BaseGraph.MAF_ins=0.0f;
jpayne@68: 		BaseGraph.MAF_noref=0.0f;
jpayne@68: 		BaseGraph.trimDepthFraction=0.3f;
jpayne@68: 		BaseGraph.trimNs=true;
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: 			
jpayne@68: 			extin=parser.extin;
jpayne@68: 
jpayne@68: 			out1=parser.out1;
jpayne@68: 			extout=parser.extout;
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		validateParams();
jpayne@68: 		adjustInterleaving(); //Make sure interleaving agrees with number of input and output files
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.FASTA, extout, true, overwrite, append, ordered);
jpayne@68: 
jpayne@68: 		//Create input FileFormat objects
jpayne@68: 		ffin=new ArrayList<FileFormat>(in.size());
jpayne@68: 		ffalt=FileFormat.testInput(alt, FileFormat.FASTA, extin, true, true);
jpayne@68: 		for(String s : in){
jpayne@68: 			FileFormat ff=FileFormat.testInput(s, FileFormat.FASTA, extin, true, true);
jpayne@68: 			ffin.add(ff);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Determine how many threads may be used
jpayne@68: 		threads=Shared.threads();
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("consensus")){
jpayne@68: 				useConsensus=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("best")){
jpayne@68: 				useConsensus=!Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("fast")){
jpayne@68: 				fast=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("minid")){
jpayne@68: 				minID=Float.parseFloat(b);
jpayne@68: 			}else if(a.equals("maxns")){
jpayne@68: 				maxns=Integer.parseInt(b);
jpayne@68: 			}else if(a.equals("minlen")){
jpayne@68: 				minlen=Integer.parseInt(b);
jpayne@68: 			}else if(a.equals("maxlen")){
jpayne@68: 				maxlen=Integer.parseInt(b);
jpayne@68: 			}else if(a.equals("in")){
jpayne@68: 				Tools.addFiles(b, in);
jpayne@68: 			}else if(a.equals("alt")){
jpayne@68: 				alt=b;
jpayne@68: 			}else if(a.equalsIgnoreCase("process16S") || a.equalsIgnoreCase("16S")){
jpayne@68: 				process16S=Parse.parseBoolean(b);
jpayne@68: 				process18S=!process16S;
jpayne@68: 			}else if(a.equalsIgnoreCase("process18S") || a.equalsIgnoreCase("18S")){
jpayne@68: 				process18S=Parse.parseBoolean(b);
jpayne@68: 				process16S=!process18S;
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 if(b==null && new File(arg).exists()){
jpayne@68: 				in.add(arg);
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: 		assert(!in.isEmpty()) : "No input file.";
jpayne@68: 		return parser;
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, in)){
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, out1, in.toArray(new String[0]))){
jpayne@68: //			throw new RuntimeException("\nSome file names were specified multiple times.\n");
jpayne@68: //		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Make sure interleaving agrees with number of input and output files */
jpayne@68: 	private void adjustInterleaving(){
jpayne@68: 		FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
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: 		assert(process16S || process18S) : "16S or 18S must be selected.";
jpayne@68: 		assert(!process16S || !process18S) : "16S or 18S are both selected; only one may be active.";
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: 		if(process16S){
jpayne@68: 			Read[] data=ProkObject.loadConsensusSequenceType("16S", true, true);
jpayne@68: 			consensus16S=data[0].bases;
jpayne@68: 			if(verbose){System.err.println("process16S: Loaded 16S consensus, length "+consensus16S.length+": "+new String(consensus16S));}
jpayne@68: 		}
jpayne@68: 		if(process18S){
jpayne@68: 			Read[] data=ProkObject.loadConsensusSequenceType("18S", true, true);
jpayne@68: 			consensus18S=data[0].bases;
jpayne@68: 			if(verbose){System.err.println("process18S: Loaded 18S consensus, length "+consensus18S.length+": "+new String(consensus18S));}
jpayne@68: 		}
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: 		//Reset counters
jpayne@68: 		readsProcessed=readsOut=0;
jpayne@68: 		basesProcessed=basesOut=0;
jpayne@68: 		
jpayne@68: 		//Align everything to global consensus
jpayne@68: 		for(FileFormat ff : ffin) {
jpayne@68: 			//Create a read input stream
jpayne@68: 			final ConcurrentReadInputStream cris=makeCris(ff);
jpayne@68: 
jpayne@68: 			//Process the reads in separate threads
jpayne@68: 			spawnThreads(cris, false);
jpayne@68: 			errorState|=ReadWrite.closeStream(cris);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(ffalt!=null){
jpayne@68: 			//Create a read input stream
jpayne@68: 			final ConcurrentReadInputStream cris=makeCris(ffalt);
jpayne@68: 
jpayne@68: 			//Process the reads in separate threads
jpayne@68: 			spawnThreads(cris, true);
jpayne@68: 			errorState|=ReadWrite.closeStream(cris);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: //		queue=new ConcurrentLinkedQueue<ArrayList<Ribo>>();
jpayne@68: //		for(Entry<Integer, ArrayList<Ribo>> e : listMap.entrySet()){
jpayne@68: //			queue.add(e.getValue());
jpayne@68: //		}
jpayne@68: //		listMap=null;
jpayne@68: 		queue=makeQueue();
jpayne@68: 		
jpayne@68: 		//Run a second pass to pick the best SSU per taxID
jpayne@68: 		spawnThreads(null, false);
jpayne@68: 		
jpayne@68: 		//Do anything necessary after processing
jpayne@68: 		if(ffout1!=null){
jpayne@68: 			//Optionally create a read output stream
jpayne@68: 			final ConcurrentReadOutputStream ros=makeCros();
jpayne@68: 			long num=0;
jpayne@68: 			for(Ribo ribo : bestList){
jpayne@68: 				Read r=ribo.r;
jpayne@68: 				readsOut++;
jpayne@68: 				basesOut+=r.length();
jpayne@68: 				ArrayList<Read> list=new ArrayList<Read>(1);
jpayne@68: 				list.add(r);
jpayne@68: 				ros.add(list, num);
jpayne@68: 				num++;
jpayne@68: 			}
jpayne@68: 			//Close the read streams
jpayne@68: 			errorState|=ReadWrite.closeStream(ros);
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: 		
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 ConcurrentLinkedQueue<ArrayList<Ribo>> makeQueue(){
jpayne@68: 		ArrayList<ArrayList<Ribo>> listList=new ArrayList<ArrayList<Ribo>>(listMap.size());
jpayne@68: 		for(Entry<Integer, ArrayList<Ribo>> e : listMap.entrySet()){
jpayne@68: 			listList.add(e.getValue());
jpayne@68: 		}
jpayne@68: 		listMap=null;
jpayne@68: 		Collections.sort(listList, new ListComparator());
jpayne@68: 		assert(listList.isEmpty() || listList.get(0).size()>=listList.get(listList.size()-1).size());
jpayne@68: 		ConcurrentLinkedQueue<ArrayList<Ribo>> q=new ConcurrentLinkedQueue<ArrayList<Ribo>>();
jpayne@68: 		for(ArrayList<Ribo> x : listList){
jpayne@68: 			q.add(x);
jpayne@68: 		}
jpayne@68: 		return q;
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) : "This should not be paired input.";
jpayne@68: 		return cris;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private ConcurrentReadOutputStream makeCros(){
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, 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, boolean altData){
jpayne@68: 		
jpayne@68: 		//Do anything necessary prior to processing
jpayne@68: 		
jpayne@68: 		//Fill a list with ProcessThreads
jpayne@68: 		if(verbose){System.err.println("Spawning "+threads+" threads.");}
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, altData));
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: 		if(verbose){System.err.println("Threads finished with success="+success+".");}
jpayne@68: 		errorState&=!success;
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: 		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: 	/*--------------------------------------------------------------*/
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_, boolean alt_){
jpayne@68: 			cris=cris_;
jpayne@68: 			tid=tid_;
jpayne@68: 			processInput=(cris!=null);
jpayne@68: 			altData=alt_;
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: 			if(processInput){
jpayne@68: 				//Process the reads
jpayne@68: 				processInner();
jpayne@68: 			}else{
jpayne@68: 				pickBest();
jpayne@68: 			}
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: 			if(verbose && tid==0){System.err.println("processInner() for tid="+tid);}
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: 				processInput(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 processInput(ListNum<Read> ln){
jpayne@68: 			if(verbose && tid==0){System.err.println("processInput() for tid="+tid);}
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: 				
jpayne@68: 				//Validate reads in worker threads
jpayne@68: 				if(!r1.validated()){r1.validate(true);}
jpayne@68: 
jpayne@68: 				//Track the initial length for statistics
jpayne@68: 				final int initialLength1=r1.length();
jpayne@68: 
jpayne@68: 				//Increment counters
jpayne@68: 				readsProcessedT++;
jpayne@68: 				basesProcessedT+=initialLength1;
jpayne@68: 				
jpayne@68: 				processRead(r1);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		void pickBest(){
jpayne@68: 			if(verbose && tid==0){System.err.println("pickBest() for tid="+tid);}
jpayne@68: 			for(ArrayList<Ribo> list=queue.poll(); list!=null; list=queue.poll()){
jpayne@68: 				Ribo best=pickBest(list);
jpayne@68: 				list.clear();
jpayne@68: 				synchronized(bestList){
jpayne@68: 					bestList.add(best);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		Ribo pickBest(ArrayList<Ribo> list){
jpayne@68: 			if(verbose && tid==0){System.err.println("pickBest(list[="+list.size()+"]) for tid="+tid);}
jpayne@68: 			assert(list!=null && list.size()>0);
jpayne@68: 			if(list.size()==1){return list.get(0);}
jpayne@68: 			Collections.sort(list);
jpayne@68: 			Collections.reverse(list);
jpayne@68: 			assert(list.get(0).product>=list.get(1).product);
jpayne@68: 			if(list.size()<3 || fast){return list.get(0);}
jpayne@68: 			
jpayne@68: 			Ribo base=list.get(0);
jpayne@68: 			int pad=Tools.max(10, (1600-base.r.length()));
jpayne@68: 			BaseGraph bg=new BaseGraph(base.r.name(), base.r.bases, base.r.quality, base.r.numericID, pad);
jpayne@68: 			for(Ribo r : list){
jpayne@68: 				bg.alignAndGenerateMatch(r.r, ssa);
jpayne@68: 			}
jpayne@68: 			Read consensus=bg.traverse();
jpayne@68: 			Ribo best;
jpayne@68: 			if(useConsensus){
jpayne@68: 				best=new Ribo(consensus, base.tid, 1);
jpayne@68: 			}else{
jpayne@68: 				for(Ribo r : list){
jpayne@68: 					float id=align(r.r.bases, consensus.bases);
jpayne@68: 					r.identity=id;
jpayne@68: 					r.product=score(r.length(), r.identity);
jpayne@68: 				}
jpayne@68: 				Collections.sort(list);
jpayne@68: 				Collections.reverse(list);
jpayne@68: 				assert(list.get(0).product>=list.get(1).product);
jpayne@68: 				best=list.get(0);
jpayne@68: 			}
jpayne@68: 			return best;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		/**
jpayne@68: 		 * Process a read or a read pair.
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(verbose && tid==0){System.err.println("processRead()");}
jpayne@68: 			if(r.length()<minlen || r.length()>maxlen){return;}
jpayne@68: 			if(maxns>=0 && r.countNocalls()>maxns){return;}
jpayne@68: 			Integer key=GiToTaxid.parseTaxidNumber(r.id, '|');
jpayne@68: 			if(verbose && tid==0){System.err.println("key="+key);}
jpayne@68: 			if(key==null || key==-1 || (altData && seenTaxID.contains(key))){return;}
jpayne@68: 			float id=align(r);
jpayne@68: 			if(id<minID){return;}
jpayne@68: 			Ribo ribo=new Ribo(r, key, id);
jpayne@68: 			
jpayne@68: 			synchronized(listMap){
jpayne@68: 				ArrayList<Ribo> list=listMap.get(key);
jpayne@68: 				if(list==null){
jpayne@68: 					list=new ArrayList<Ribo>(8);
jpayne@68: 					listMap.put(key, list);
jpayne@68: 				}
jpayne@68: 				list.add(ribo);
jpayne@68: 				if(!altData){seenTaxID.add(key);}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		float align(Read r){
jpayne@68: 			float a=(process16S ? align(r.bases, consensus16S) : 0);
jpayne@68: 			float b=(process18S ? align(r.bases, consensus18S) : 0);
jpayne@68: 			if(verbose && tid==0){System.err.println("Aligned; a="+a+", b="+b);}
jpayne@68: 			return Tools.max(a, b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		float align(byte[] query, byte[] ref){
jpayne@68: 			int a=0, b=ref.length-1;
jpayne@68: 			int[] max=ssa.fillUnlimited(query, ref, a, b, -9999);
jpayne@68: 			if(max==null){return 0;}
jpayne@68: 			
jpayne@68: 			final int rows=max[0];
jpayne@68: 			final int maxCol=max[1];
jpayne@68: 			final int maxState=max[2];
jpayne@68: 			final float id=ssa.tracebackIdentity(query, ref, a, b, rows, maxCol, maxState, null);
jpayne@68: 			return id;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		SingleStateAlignerFlat2 ssa=new SingleStateAlignerFlat2();
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: 		/** True only if this thread has completed successfully */
jpayne@68: 		boolean success=false;
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: 		//Run mode
jpayne@68: 		final boolean processInput;
jpayne@68: 		final boolean altData;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private class Ribo implements Comparable<Ribo>{
jpayne@68: 		Ribo(Read r_, int tid_, float identity_){
jpayne@68: 			r=r_;
jpayne@68: 			tid=tid_;
jpayne@68: 			identity=identity_;
jpayne@68: 			product=score(r.length(), identity);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		@Override
jpayne@68: 		public int compareTo(Ribo b) {
jpayne@68: 			if(b.product>product){return -1;}
jpayne@68: 			else if(b.product<product){return 1;}
jpayne@68: 			else if(b.r.length()>r.length()){return -1;}
jpayne@68: 			else if(b.r.length()<r.length()){return 1;}
jpayne@68: 			return 0;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		int length(){return r.length();}
jpayne@68: 		
jpayne@68: 		Read r;
jpayne@68: 		int tid;
jpayne@68: 		float identity;
jpayne@68: 		float product;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private class ListComparator implements Comparator<ArrayList<Ribo>> {
jpayne@68: 
jpayne@68: 		@Override
jpayne@68: 		public int compare(ArrayList<Ribo> a, ArrayList<Ribo> b) {
jpayne@68: 			return a.size()>b.size() ? -1 : a.size()<b.size() ? 1 : 0;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private float lengthMult(int len){
jpayne@68: 		int idealLength=idealLength();
jpayne@68: 		int max=Tools.max(len, idealLength, 1);
jpayne@68: 		int min=Tools.min(len, idealLength);
jpayne@68: 		return min/(float)max;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private float score(int len, float identity){
jpayne@68: 		return lengthMult(len)*identity;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** Primary input file path */
jpayne@68: 	private ArrayList<String> in=new ArrayList<String>();
jpayne@68: 	
jpayne@68: 	/** Alternate input file path */
jpayne@68: 	private String alt=null;
jpayne@68: 	
jpayne@68: 	/** Primary output file path */
jpayne@68: 	private String out1=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: 	ArrayList<Ribo> bestList=new ArrayList<Ribo>();
jpayne@68: 	HashMap<Integer, ArrayList<Ribo>> listMap=new HashMap<Integer, ArrayList<Ribo>>(100000);
jpayne@68: 	ConcurrentLinkedQueue<ArrayList<Ribo>> queue;
jpayne@68: 	
jpayne@68: 	
jpayne@68: 	IntHashSet seenTaxID=new IntHashSet(1000000);
jpayne@68: 	
jpayne@68: 	byte[] consensus16S;
jpayne@68: 	byte[] consensus18S;
jpayne@68: 	
jpayne@68: 	int idealLength(){
jpayne@68: 		if(process16S){return consensus16S.length;}
jpayne@68: 		return consensus18S.length;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	boolean useConsensus=false;
jpayne@68: 	boolean fast=false;
jpayne@68: 	int maxns=-1;
jpayne@68: 	int minlen=1;
jpayne@68: 	int maxlen=4000;
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: 	private float minID=0.62f;
jpayne@68: 	
jpayne@68: 	private boolean process16S=true;
jpayne@68: 	private boolean process18S=false;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Final Fields         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/** Primary input file */
jpayne@68: 	private final ArrayList<FileFormat> ffin;
jpayne@68: 	private final FileFormat ffalt;
jpayne@68: 	
jpayne@68: 	/** Primary output file */
jpayne@68: 	private final FileFormat ffout1;
jpayne@68: 	
jpayne@68: 	final int threads;
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: }