current/template/A_SampleSamStreamer.java

package template;

import java.io.PrintStream;
import java.util.ArrayList;

import fileIO.ByteFile;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Parse;
import shared.Parser;
import shared.PreParser;
import shared.ReadStats;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import stream.ConcurrentReadInputStream;
import stream.ConcurrentReadOutputStream;
import stream.FastaReadInputStream;
import stream.Read;
import stream.SamLine;
import stream.SamReadStreamer;
import stream.SamStreamer;
import structures.ListNum;
import var2.Realigner;
import var2.SamFilter;
import var2.ScafMap;

/**
 * This class does nothing.
 * It is designed to be easily modified into a program
 * that processes reads in multiple threads, by
 * filling in the processRead method.
 *
 * @author Brian Bushnell
 * @date September 6, 2019
 *
 */
public class A_SampleSamStreamer implements Accumulator<A_SampleSamStreamer.ProcessThread> {

	/*--------------------------------------------------------------*/
	/*----------------        Initialization        ----------------*/
	/*--------------------------------------------------------------*/

	/**
	 * Code entrance from the command line.
	 * @param args Command line arguments
	 */
	public static void main(String[] args){
		//Start a timer immediately upon code entrance.
		Timer t=new Timer();

		//Create an instance of this class
		A_SampleSamStreamer x=new A_SampleSamStreamer(args);

		//Run the object
		x.process(t);

		//Close the print stream if it was redirected
		Shared.closeStream(x.outstream);
	}

	/**
	 * Constructor.
	 * @param args Command line arguments
	 */
	public A_SampleSamStreamer(String[] args){

		{//Preparse block for help, config files, and outstream
			PreParser pp=new PreParser(args, getClass(), false);
			args=pp.args;
			outstream=pp.outstream;
		}

		//Set shared static variables prior to parsing
		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
		ReadWrite.MAX_ZIP_THREADS=Shared.threads();

//		samFilter.includeUnmapped=false;
//		samFilter.includeSupplimentary=false;
//		samFilter.includeDuplicate=false;
//		samFilter.includeNonPrimary=false;
//		samFilter.includeQfail=false;
//		samFilter.minMapq=4;

		{//Parse the arguments
			final Parser parser=parse(args);

			Parser.processQuality();

			maxReads=parser.maxReads;
			overwrite=ReadStats.overwrite=parser.overwrite;
			append=ReadStats.append=parser.append;

			in=parser.in1;
			extin=parser.extin;

			out=parser.out1;
			extout=parser.extout;
		}

		{
//			if("auto".equalsIgnoreCase(atomic)){Scaffold.setCA3A(Shared.threads()>8);}
//			else{Scaffold.setCA3A(Parse.parseBoolean(atomic));}

			if(ploidy<1){System.err.println("WARNING: ploidy not set; assuming ploidy=1."); ploidy=1;}
			samFilter.setSamtoolsFilter();

			streamerThreads=Tools.max(1, Tools.min(streamerThreads, Shared.threads()));
			assert(streamerThreads>0) : streamerThreads;
		}

		validateParams();
		fixExtensions(); //Add or remove .gz or .bz2 as needed
		checkFileExistence(); //Ensure files can be read and written
		checkStatics(); //Adjust file-related static fields as needed for this program

		//Create output FileFormat objects
		ffout=FileFormat.testOutput(out, FileFormat.SAM, extout, true, overwrite, append, ordered);
		assert(false) : "TODO: Default output format might be fasta.";

		//Create input FileFormat objects
		ffin=FileFormat.testInput(in, FileFormat.SAM, extin, true, true);
		ffref=FileFormat.testInput(ref, FileFormat.FASTA, null, true, true);
	}

	/*--------------------------------------------------------------*/
	/*----------------    Initialization Helpers    ----------------*/
	/*--------------------------------------------------------------*/

	/** Parse arguments from the command line */
	private Parser parse(String[] args){

		//Create a parser object
		Parser parser=new Parser();

		//Set any necessary Parser defaults here
		//parser.foo=bar;

		//Parse each argument
		for(int i=0; i<args.length; i++){
			String arg=args[i];

			//Break arguments into their constituent parts, in the form of "a=b"
			String[] split=arg.split("=");
			String a=split[0].toLowerCase();
			String b=split.length>1 ? split[1] : null;
			if(b!=null && b.equalsIgnoreCase("null")){b=null;}

			if(a.equals("verbose")){
				verbose=Parse.parseBoolean(b);
			}else if(a.equals("ref")){
				ref=b;
			}else if(a.equals("ordered")){
				ordered=Parse.parseBoolean(b);
			}else if(a.equals("realign")){
				realign=Parse.parseBoolean(b);
			}else if(a.equals("ploidy")){
				ploidy=Integer.parseInt(b);
			}else if(a.equals("clearfilters")){
				if(Parse.parseBoolean(b)){
					samFilter.clear();
				}
			}else if(a.equals("parse_flag_goes_here")){
				long fake_variable=Parse.parseKMG(b);
				//Set a variable here
			}else if(samFilter.parse(arg, a, b)){
				//do nothing
			}else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
				//do nothing
			}else{
				outstream.println("Unknown parameter "+args[i]);
				assert(false) : "Unknown parameter "+args[i];
			}
		}

		return parser;
	}

	/** Add or remove .gz or .bz2 as needed */
	private void fixExtensions(){
		in=Tools.fixExtension(in);
		ref=Tools.fixExtension(ref);
	}

	/** Ensure files can be read and written */
	private void checkFileExistence(){

		//Ensure there is an input file
		if(in==null){throw new RuntimeException("Error - an input file is required.");}

		//Ensure there is an input file
		assert(false) : "TODO: Check.";
		if(ref==null){throw new RuntimeException("Error - a reference file is required.");}

		//Ensure output files can be written
		if(!Tools.testOutputFiles(overwrite, append, false, out)){
			outstream.println((out==null)+", "+out);
			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output file "+out+"\n");
		}

		//Ensure input files can be read
		if(!Tools.testInputFiles(false, true, in, ref)){
			throw new RuntimeException("\nCan't read some input files.\n");
		}

		//Ensure that no file was specified multiple times
		if(!Tools.testForDuplicateFiles(true, in, ref, out)){
			throw new RuntimeException("\nSome file names were specified multiple times.\n");
		}
	}

	/** Adjust file-related static fields as needed for this program */
	private static void checkStatics(){
		//Adjust the number of threads for input file reading
		if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
			ByteFile.FORCE_MODE_BF2=true;
		}

		assert(FastaReadInputStream.settingsOK());
	}

	/** Ensure parameter ranges are within bounds and required parameters are set */
	private boolean validateParams(){
//		assert(minfoo>0 && minfoo<=maxfoo) : minfoo+", "+maxfoo;
		assert(false) : "TODO";
		return true;
	}

	/*--------------------------------------------------------------*/
	/*----------------         Outer Methods        ----------------*/
	/*--------------------------------------------------------------*/

	/** Create read streams and process all data */
	void process(Timer t){

		//Turn off read validation in the input threads to increase speed
		final boolean vic=Read.VALIDATE_IN_CONSTRUCTOR;
		Read.VALIDATE_IN_CONSTRUCTOR=Shared.threads()<4;

		//Create a read input stream
		final SamStreamer ss=makeStreamer(ffin);

		//Load reference, if desired (and if present);
		loadScafMapFromReference();
//		loadReferenceCustom();

		//Optionally create a read output stream
		final ConcurrentReadOutputStream ros=makeCros();

		//Reset counters
		readsProcessed=readsOut=0;
		basesProcessed=basesOut=0;

		//Process the reads in separate threads
		spawnThreads(ss, ros);

		if(verbose){outstream.println("Finished; closing streams.");}

		//Write anything that was accumulated by ReadStats
		errorState|=ReadStats.writeAll();
		//Close the read streams
		errorState|=ReadWrite.closeStream(ros);

		//Reset read validation
		Read.VALIDATE_IN_CONSTRUCTOR=vic;

		//Report timing and results
		t.stop();
		outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
		outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false));

		//Throw an exception of there was an error in a thread
		if(errorState){
			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
		}
	}

	private void loadScafMapFromReference(){
		if(loadedRef){return;}
		assert(ref!=null);
		scafMap=ScafMap.loadReference(ref, scafMap, samFilter, true);
		if(realign){Realigner.map=scafMap;}
		loadedRef=true;
	}

	private void loadReferenceCustom(){
		ConcurrentReadInputStream cris=makeRefCris();
		for(ListNum<Read> ln=cris.nextList(); ln!=null && ln.size()>0; ln=cris.nextList()) {
			//Do something
			assert(false) : "TODO";
		}
	}

	private ConcurrentReadInputStream makeRefCris(){
		ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffref, null);
		cris.start(); //Start the stream
		if(verbose){outstream.println("Started cris");}
		boolean paired=cris.paired();
		assert(!paired) : "References should not be paired.";
		return cris;
	}

	private SamStreamer makeStreamer(FileFormat ff){
		if(ff==null){return null;}
		SamStreamer ss=new SamReadStreamer(ff, streamerThreads, true, maxReads);
		ss.start(); //Start the stream
		if(verbose){outstream.println("Started Streamer");}
		return ss;
	}

	private ConcurrentReadOutputStream makeCros(){
		if(ffout==null){return null;}

		//Select output buffer size based on whether it needs to be ordered
		final int buff=(ordered ? Tools.mid(16, 128, (Shared.threads()*2)/3) : 8);

		final ConcurrentReadOutputStream ros=ConcurrentReadOutputStream.getStream(ffout, null, buff, null, false);
		ros.start(); //Start the stream
		return ros;
	}

	/*--------------------------------------------------------------*/
	/*----------------       Thread Management      ----------------*/
	/*--------------------------------------------------------------*/

	/** Spawn process threads */
	private void spawnThreads(final SamStreamer ss, final ConcurrentReadOutputStream ros){

		//Do anything necessary prior to processing

		//Determine how many threads may be used
		final int threads=Shared.threads();

		//Fill a list with ProcessThreads
		ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
		for(int i=0; i<threads; i++){
			alpt.add(new ProcessThread(ss, ros, i));
		}

		//Start the threads
		for(ProcessThread pt : alpt){
			pt.start();
		}

		//Wait for threads to finish
		boolean success=ThreadWaiter.waitForThreads(alpt, this);
		errorState&=!success;

		//Do anything necessary after processing

	}

	@Override
	public final void accumulate(ProcessThread pt){
		readsProcessed+=pt.readsProcessedT;
		basesProcessed+=pt.basesProcessedT;
		readsOut+=pt.readsOutT;
		basesOut+=pt.basesOutT;
		errorState|=(!pt.success);
	}

	@Override
	public final boolean success(){return !errorState;}

	/*--------------------------------------------------------------*/
	/*----------------         Inner Methods        ----------------*/
	/*--------------------------------------------------------------*/

	/*--------------------------------------------------------------*/
	/*----------------         Inner Classes        ----------------*/
	/*--------------------------------------------------------------*/

	/** This class is static to prevent accidental writing to shared variables.
	 * It is safe to remove the static modifier. */
	class ProcessThread extends Thread {

		//Constructor
		ProcessThread(final SamStreamer ss_, final ConcurrentReadOutputStream ros_, final int tid_){
			ss=ss_;
			ros=ros_;
			tid=tid_;
			realigner=(realign ? new Realigner() : null);
		}

		//Called by start()
		@Override
		public void run(){
			//Do anything necessary prior to processing

			//Process the reads
			processInner();

			//Do anything necessary after processing

			//Indicate successful exit status
			success=true;
		}

		/** Iterate through the reads */
		void processInner(){

			//Grab and process all lists
			for(ListNum<Read> ln=ss.nextReads(); ln!=null; ln=ss.nextReads()){
//				if(verbose){outstream.println("Got list of size "+list.size());} //Disabled due to non-static access

				processList(ln);
			}

		}

		void processList(ListNum<Read> ln){

			//Grab the actual read list from the ListNum
			final ArrayList<Read> reads=ln.list;

			//Loop through each read in the list
			for(int idx=0; idx<reads.size(); idx++){
				final Read r=reads.get(idx);

				//Validate reads in worker threads
				if(!r.validated()){r.validate(true);}

				//Track the initial length for statistics
				final int initialLength=r.length();

				//Increment counters
				readsProcessedT+=r.pairCount();
				basesProcessedT+=initialLength;

				{
					//Reads are processed in this block.
					boolean keep=processRead(r);

					if(!keep){reads.set(idx, null);}
					else{
						readsOutT++;
						basesOutT+=r.length();
					}
				}
			}

			//Output reads to the output stream
			if(ros!=null){ros.add(reads, ln.id);}
		}

		/**
		 * Process a read or a read pair.
		 * @param r Read 1
		 * @param r2 Read 2 (may be null)
		 * @return True if the reads should be kept, false if they should be discarded.
		 */
		boolean processRead(final Read r){
			if(r.bases==null || r.length()<=1){return false;}
			final SamLine sl=r.samline;
			if(samFilter!=null && !samFilter.passesFilter(sl)){return false;}

//			System.err.println("A: "+sl);

//			final SamLine oldSL=new SamLine(sl);
//			final Read oldRead=r.clone();

			assert(false) : "TODO";
			return true;
		}

		/** Number of reads processed by this thread */
		protected long readsProcessedT=0;
		/** Number of bases processed by this thread */
		protected long basesProcessedT=0;

		/** Number of reads retained by this thread */
		protected long readsOutT=0;
		/** Number of bases retained by this thread */
		protected long basesOutT=0;

		/** True only if this thread has completed successfully */
		boolean success=false;

		/** Shared input stream */
		private final SamStreamer ss;
		/** Shared output stream */
		private final ConcurrentReadOutputStream ros;
		/** Thread ID */
		final int tid;
		/** For realigning reads */
		final Realigner realigner;
	}

	/*--------------------------------------------------------------*/
	/*----------------            Fields            ----------------*/
	/*--------------------------------------------------------------*/

	/** Primary input file path */
	private String in=null;
	/** Secondary input file path */
	private String ref=null;

	/** Primary output file path */
	private String out=null;

	/** Override input file extension */
	private String extin=null;
	/** Override output file extension */
	private String extout=null;

	/*--------------------------------------------------------------*/

	/** Number of reads processed */
	protected long readsProcessed=0;
	/** Number of bases processed */
	protected long basesProcessed=0;

	/** Number of reads retained */
	protected long readsOut=0;
	/** Number of bases retained */
	protected long basesOut=0;

	/** Quit after processing this many input reads; -1 means no limit */
	private long maxReads=-1;

	/*--------------------------------------------------------------*/

	/** Threads dedicated to reading the sam file */
	private int streamerThreads=SamStreamer.DEFAULT_THREADS;

	private boolean loadedRef=false;

	private boolean realign=false;

	private int ploidy=1;

	public ScafMap scafMap;
	public final SamFilter samFilter=new SamFilter();

	/*--------------------------------------------------------------*/
	/*----------------         Final Fields         ----------------*/
	/*--------------------------------------------------------------*/

	/** Primary input file */
	private final FileFormat ffin;
	/** Secondary input file */
	private final FileFormat ffref;

	/** Primary output file */
	private final FileFormat ffout;

	/*--------------------------------------------------------------*/
	/*----------------        Common Fields         ----------------*/
	/*--------------------------------------------------------------*/

	/** Print status messages to this output stream */
	private PrintStream outstream=System.err;
	/** Print verbose messages */
	public static boolean verbose=false;
	/** True if an error was encountered */
	public boolean errorState=false;
	/** Overwrite existing output files */
	private boolean overwrite=false;
	/** Append to existing output files */
	private boolean append=false;
	/** Reads are output in input order */
	private boolean ordered=false;

}