current/jgi/AdjustHomopolymers.java

package jgi;

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

import dna.AminoAcid;
import fileIO.ByteFile;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.KillSwitch;
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.FASTQ;
import stream.FastaReadInputStream;
import stream.Read;
import structures.ByteBuilder;
import structures.ListNum;

/**
 * This class does nothing.
 * It is designed to be easily modified into a program
 * that processes reads in a single thread.
 *
 * @author Brian Bushnell
 * @date June 20, 2014
 *
 */
public class AdjustHomopolymers {

	/*--------------------------------------------------------------*/
	/*----------------        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
		AdjustHomopolymers x=new AdjustHomopolymers(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 AdjustHomopolymers(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();
		Shared.capBuffers(4); //Only for singlethreaded programs

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

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

			in1=parser.in1;
			in2=parser.in2;
			qfin1=parser.qfin1;
			qfin2=parser.qfin2;
			extin=parser.extin;

			out1=parser.out1;
			out2=parser.out2;
			qfout1=parser.qfout1;
			qfout2=parser.qfout2;
			extout=parser.extout;
		}

		assert(rate!=0) : "'rate' should be set to a positive or negative value, such as rate=0.1 to expand homopolymers by 10%.";

		doPoundReplacement(); //Replace # with 1 and 2
		adjustInterleaving(); //Make sure interleaving agrees with number of input and output files
		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
		ffout1=FileFormat.testOutput(out1, FileFormat.FASTQ, extout, true, overwrite, append, ordered);
		ffout2=FileFormat.testOutput(out2, FileFormat.FASTQ, extout, true, overwrite, append, ordered);

		//Create input FileFormat objects
		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
		ffin2=FileFormat.testInput(in2, FileFormat.FASTQ, extin, 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("rate")){
				rate=Float.parseFloat(b);
			}else if(a.equals("parse_flag_goes_here")){
				long fake_variable=Parse.parseKMG(b);
				//Set a variable here
			}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;
	}

	/** Replace # with 1 and 2 in headers */
	private void doPoundReplacement(){
		//Do input file # replacement
		if(in1!=null && in2==null && in1.indexOf('#')>-1 && !new File(in1).exists()){
			in2=in1.replace("#", "2");
			in1=in1.replace("#", "1");
		}

		//Do output file # replacement
		if(out1!=null && out2==null && out1.indexOf('#')>-1){
			out2=out1.replace("#", "2");
			out1=out1.replace("#", "1");
		}

		//Ensure there is an input file
		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}

		//Ensure out2 is not set without out1
		if(out1==null && out2!=null){throw new RuntimeException("Error - cannot define out2 without defining out1.");}
	}

	/** Add or remove .gz or .bz2 as needed */
	private void fixExtensions(){
		in1=Tools.fixExtension(in1);
		in2=Tools.fixExtension(in2);
		qfin1=Tools.fixExtension(qfin1);
		qfin2=Tools.fixExtension(qfin2);
	}

	/** Ensure files can be read and written */
	private void checkFileExistence(){
		//Ensure output files can be written
		if(!Tools.testOutputFiles(overwrite, append, false, out1, out2)){
			outstream.println((out1==null)+", "+(out2==null)+", "+out1+", "+out2);
			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+", "+out2+"\n");
		}

		//Ensure input files can be read
		if(!Tools.testInputFiles(false, true, in1, in2)){
			throw new RuntimeException("\nCan't read some input files.\n");
		}

		//Ensure that no file was specified multiple times
		if(!Tools.testForDuplicateFiles(true, in1, in2, out1, out2)){
			throw new RuntimeException("\nSome file names were specified multiple times.\n");
		}
	}

	/** Make sure interleaving agrees with number of input and output files */
	private void adjustInterleaving(){
		//Adjust interleaved detection based on the number of input files
		if(in2!=null){
			if(FASTQ.FORCE_INTERLEAVED){outstream.println("Reset INTERLEAVED to false because paired input files were specified.");}
			FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
		}

		//Adjust interleaved settings based on number of output files
		if(!setInterleaved){
			assert(in1!=null && (out1!=null || out2==null)) : "\nin1="+in1+"\nin2="+in2+"\nout1="+out1+"\nout2="+out2+"\n";
			if(in2!=null){ //If there are 2 input streams.
				FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
				outstream.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
			}else{ //There is one input stream.
				if(out2!=null){
					FASTQ.FORCE_INTERLEAVED=true;
					FASTQ.TEST_INTERLEAVED=false;
					outstream.println("Set INTERLEAVED to "+FASTQ.FORCE_INTERLEAVED);
				}
			}
		}
	}

	/** 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());
	}

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

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

		//Create a read input stream
		final ConcurrentReadInputStream cris=makeCris();

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

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

		//Process the read stream
		processInner(cris, ros);

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

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

		//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.");
		}
	}

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

	private ConcurrentReadInputStream makeCris(){
		ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
		cris.start(); //Start the stream
		if(verbose){outstream.println("Started cris");}
		boolean paired=cris.paired();
		if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
		return cris;
	}

	private ConcurrentReadOutputStream makeCros(boolean pairedInput){
		if(ffout1==null){return null;}

		//Select output buffer size based on whether it needs to be ordered
		final int buff=4;

		//Notify user of output mode
		if(pairedInput && out2==null && (in1!=null && !ffin1.samOrBam() && !ffout1.samOrBam())){
			outstream.println("Writing interleaved.");
		}

		final ConcurrentReadOutputStream ros=ConcurrentReadOutputStream.getStream(ffout1, ffout2, qfout1, qfout2, buff, null, false);
		ros.start(); //Start the stream
		return ros;
	}

	/** Iterate through the reads */
	void processInner(final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros){

		//Do anything necessary prior to processing

		{
			//Grab the first ListNum of reads
			ListNum<Read> ln=cris.nextList();

			//Check to ensure pairing is as expected
			if(ln!=null && !ln.isEmpty()){
				Read r=ln.get(0);
				assert(ffin1.samOrBam() || (r.mate!=null)==cris.paired());
			}

			//As long as there is a nonempty read list...
			while(ln!=null && ln.size()>0){
//				if(verbose){outstream.println("Fetched "+reads.size()+" reads.");} //Disabled due to non-static access

				processList(ln, cris, ros);

				//Fetch a new list
				ln=cris.nextList();
			}

			//Notify the input stream that the final list was used
			if(ln!=null){
				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
			}
		}

		//Do anything necessary after processing

	}

	/**
	 * Process a list of Reads.
	 * @param ln The list.
	 * @param cris Read Input Stream
	 * @param ros Read Output Stream for reads that will be retained
	 */
	void processList(ListNum<Read> ln, final ConcurrentReadInputStream cris, final ConcurrentReadOutputStream ros){

		//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 r1=reads.get(idx);
			final Read r2=r1.mate;

			//Validate reads in worker threads
			if(!r1.validated()){r1.validate(true);}
			if(r2!=null && !r2.validated()){r2.validate(true);}

			//Track the initial length for statistics
			final int initialLength1=r1.length();
			final int initialLength2=r1.mateLength();

			//Increment counters
			readsProcessed+=r1.pairCount();
			basesProcessed+=initialLength1+initialLength2;

			{
				//Reads are processed in this block.
				boolean keep=processReadPair(r1, r2);

				if(!keep){reads.set(idx, null);}
				else{
					readsOut+=r1.pairCount();
					basesOut+=r1.pairLength();
				}
			}
		}

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

		//Notify the input stream that the list was used
		cris.returnList(ln);
//		if(verbose){outstream.println("Returned a list.");} //Disabled due to non-static access
	}


	/**
	 * Process a single read pair.
	 * @param r1 Read 1
	 * @param r2 Read 2 (may be null)
	 * @return True if the reads should be kept, false if they should be discarded.
	 */
	boolean processReadPair(final Read r1, final Read r2){
		processRead(r1);
		processRead(r2);
		return true;
	}

	void processRead(final Read r){
		if(r==null){return;}
		bbBases.clear();
		bbQuals.clear();
		final byte[] bases=r.bases;
		final byte[] quals=(r.quality==null ? fakeQuality(bases.length) : r.quality);

		byte prevBase='?';
		byte prevQual=20;
		byte streak=0;
		for(int i=0; i<bases.length; i++){
			final byte b=bases[i];
			final byte q=quals[i];
			bbBases.append(b);
			bbQuals.append(q);
			if(b==prevBase){
				streak++;
			}else{
				int adjustment=AminoAcid.isFullyDefined(prevBase) ? (int)(rate*streak) : 0;
				if(adjustment<0){
					bbBases.length+=adjustment;
					bbQuals.length+=adjustment;
				}else{
					for(; adjustment>0; adjustment--){
						bbBases.append(prevBase);
						bbQuals.append(prevQual);
					}
				}
				streak=1;
			}
			prevBase=b;
			prevQual=q;
		}
		if(bbBases.length()!=r.length()){
			r.bases=bbBases.toBytes();
			r.quality=(r.quality==null ? null : bbQuals.toBytes());
		}
	}

	private byte[] fakeQuality(int minlen){
		if(fakeQuality.length<minlen){
			fakeQuality=KillSwitch.allocByte1D(minlen+10);
			Arrays.fill(fakeQuality, Shared.FAKE_QUAL);
		}
		return fakeQuality;
	}

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

	/** Primary input file path */
	private String in1=null;
	/** Secondary input file path */
	private String in2=null;

	private String qfin1=null;
	private String qfin2=null;

	/** Primary output file path */
	private String out1=null;
	/** Secondary output file path */
	private String out2=null;

	private String qfout1=null;
	private String qfout2=null;

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

	/** Whether interleaved was explicitly set. */
	private boolean setInterleaved=false;

	private ByteBuilder bbBases=new ByteBuilder();
	private ByteBuilder bbQuals=new ByteBuilder();

	private float rate=0.0f;

	private byte[] fakeQuality=new byte[0];

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

	/** 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;

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

	/** Primary input file */
	private final FileFormat ffin1;
	/** Secondary input file */
	private final FileFormat ffin2;

	/** Primary output file */
	private final FileFormat ffout1;
	/** Secondary output file */
	private final FileFormat ffout2;

	/*--------------------------------------------------------------*/
	/*----------------        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;
	/** This flag has no effect on singlethreaded programs */
	private final boolean ordered=false;

}