package jgi;

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

import stream.ConcurrentGenericReadInputStream;
import stream.ConcurrentReadInputStream;
import stream.FASTQ;
import stream.FastaReadInputStream;
import stream.ConcurrentReadOutputStream;
import stream.Read;
import structures.ListNum;
import fileIO.ByteFile;
import fileIO.ByteFile1;
import fileIO.ByteFile2;
import fileIO.ReadWrite;
import shared.Parser;
import shared.ReadStats;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import fileIO.FileFormat;

/**
 * @author Brian Bushnell
 * @date Sep 11, 2012
 *
 */
public class MergeBarcodes {

	public static void main(String[] args){
		Timer t=new Timer();
		MergeBarcodes mb=new MergeBarcodes(args);
		HashMap<String, Read> map=mb.loadBarcodes();
		mb.mergeWithMap(t, map);
	}
	
	public MergeBarcodes(String[] args){
		
		args=Parser.parseConfig(args);
		if(Parser.parseHelp(args, true)){
			printOptions();
			System.exit(0);
		}
		
		for(String s : args){if(s.startsWith("out=standardout") || s.startsWith("out=stdout")){outstream=System.err;}}
		outstream.println("Executing "+getClass().getName()+" "+Arrays.toString(args)+"\n");
		
		boolean setInterleaved=false; //Whether it was explicitly set.

		
		
		Shared.capBufferLen(200);
		Shared.capBuffers(4);
		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
		
		
		Parser parser=new Parser();
		for(int i=0; i<args.length; i++){
			String arg=args[i];
			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;}
			while(a.startsWith("-")){a=a.substring(1);} //In case people use hyphens

			if(parser.parse(arg, a, b)){
				//do nothing
			}else if(a.equals("verbose")){
				verbose=Tools.parseBoolean(b);
				ByteFile1.verbose=verbose;
				ByteFile2.verbose=verbose;
				stream.FastaReadInputStream.verbose=verbose;
				ConcurrentGenericReadInputStream.verbose=verbose;
//				align2.FastaReadInputStream2.verbose=verbose;
				stream.FastqReadInputStream.verbose=verbose;
				ReadWrite.verbose=verbose;
			}else if(a.equals("barcode") || a.equals("bar") || a.equals("index")){
				inbar=b;
			}else if(a.equals("addslash")){
				addslash=Tools.parseBoolean(b);
			}else if(a.equals("addcolon")){
				addcolon=Tools.parseBoolean(b);
			}else if(a.equals("rcompmate") || a.equals("rcm")){
				reverseComplimentMate=Tools.parseBoolean(b);
				outstream.println("Set RCOMPMATE to "+reverseComplimentMate);
			}else if(a.equals("rcomp") || a.equals("rc")){
				reverseCompliment=Tools.parseBoolean(b);
				outstream.println("Set RCOMP to "+reverseCompliment);
			}else if(parser.in1==null && i==0 && !arg.contains("=") && (arg.toLowerCase().startsWith("stdin") || new File(arg).exists())){
				parser.in1=arg;
			}else{
				outstream.println("Unknown parameter "+args[i]);
				assert(false) : "Unknown parameter "+args[i];
				//				throw new RuntimeException("Unknown parameter "+args[i]);
			}
		}
		
		{//Process parser fields
			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;

			out1=parser.out1;
			out2=parser.out2;
			qfout1=parser.qfout1;
			qfout2=parser.qfout2;
			
			extin=parser.extin;
			extout=parser.extout;
		}
		
		if(in1!=null && in2==null && in1.indexOf('#')>-1 && !new File(in1).exists()){
			in2=in1.replace("#", "2");
			in1=in1.replace("#", "1");
		}
		if(out1!=null && out2==null && out1.indexOf('#')>-1){
			out2=out1.replace("#", "2");
			out1=out1.replace("#", "1");
		}
		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;
		}
		
		assert(FastaReadInputStream.settingsOK());
		
		if(in1==null){
			printOptions();
			throw new RuntimeException("Error - at least one input file is required.");
		}
		if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
			ByteFile.FORCE_MODE_BF2=true;
		}
		
		if(out1==null){
			if(out2!=null){
				printOptions();
				throw new RuntimeException("Error - cannot define out2 without defining out1.");
			}
			if(!parser.setOut){
				System.err.println("No output stream specified.  To write to stdout, please specify 'out=stdout.fq' or similar.");
//				out1="stdout";
			}
		}
		
		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);
				}
			}
		}

		if(out1!=null && out1.equalsIgnoreCase("null")){out1=null;}
		if(out2!=null && out2.equalsIgnoreCase("null")){out2=null;}
		
		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");
		}
		
		assert(inbar!=null) : "Must specify a barcode file.";
		ffbar=FileFormat.testInput(inbar, FileFormat.FASTQ, extin, true, true);
		
		ffout1=FileFormat.testOutput(out1, FileFormat.FASTQ, extout, true, overwrite, append, false);
		ffout2=FileFormat.testOutput(out2, FileFormat.FASTQ, extout, true, overwrite, append, false);

		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
		ffin2=FileFormat.testInput(in2, FileFormat.FASTQ, extin, true, true);
	}
	
	public HashMap<String, Read> loadBarcodes(){
		return loadBarcodes(outstream, ffbar, maxReads);
	}
	
	public static HashMap<String, Read> loadBarcodes(PrintStream outstream, FileFormat ffbar, long maxReads){
		
		Timer t=new Timer();
		
		final boolean oldForceInterleaved=FASTQ.FORCE_INTERLEAVED;
		final boolean oldTestInterleaved=FASTQ.TEST_INTERLEAVED;
		
		FASTQ.FORCE_INTERLEAVED=false;
		FASTQ.TEST_INTERLEAVED=false;
		
		HashMap<String, Read> map=new HashMap<String, Read>(0x10000-1);
		
		final ConcurrentReadInputStream cris;
		{
			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffbar, null, null, null);
			if(verbose){outstream.println("Started cris for barcodes");}
			cris.start(); //4567
		}
//		final boolean paired=cris.paired();
//		if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
		
		long readsProcessed=0;
		long basesProcessed=0;
		
		{
			
			ListNum<Read> ln=cris.nextList();
			ArrayList<Read> reads=(ln!=null ? ln.list : null);
			
//			outstream.println("Fetched "+reads);
			
			if(reads!=null && !reads.isEmpty()){
				Read r=reads.get(0);
				assert((r.mate!=null)==cris.paired());
			}

			while(reads!=null && reads.size()>0){
				
				for(int idx=0; idx<reads.size(); idx++){
					final Read r1=reads.get(idx);
					final Read r2=r1.mate;
					
					if(r1.id.indexOf(' ')>=0){r1.id=r1.id.split(" ")[0];}
					
					final int initialLength1=r1.length();
					final int initialLength2=(r1.mateLength());
					
					{
						readsProcessed++;
						basesProcessed+=initialLength1;
					}
					if(r2!=null){
						readsProcessed++;
						basesProcessed+=initialLength2;
					}
					
					map.put(r1.id, r1);
				}

				cris.returnList(ln.id, ln.list.isEmpty());
				ln=cris.nextList();
				reads=(ln!=null ? ln.list : null);
			}
			if(ln!=null){
				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
			}
		}
		
		boolean errorState=false;
		errorState|=ReadWrite.closeStream(cris);
		
		t.stop();
		
		double rpnano=readsProcessed/(double)(t.elapsed);
		double bpnano=basesProcessed/(double)(t.elapsed);

		String rpstring=(readsProcessed<100000 ? ""+readsProcessed : readsProcessed<100000000 ? (readsProcessed/1000)+"k" : (readsProcessed/1000000)+"m");
		String bpstring=(basesProcessed<100000 ? ""+basesProcessed : basesProcessed<100000000 ? (basesProcessed/1000)+"k" : (basesProcessed/1000000)+"m");

		while(rpstring.length()<8){rpstring=" "+rpstring;}
		while(bpstring.length()<8){bpstring=" "+bpstring;}
		
		outstream.println("Loaded barcodes.");
		outstream.println("Time:                         \t"+t);
		outstream.println("Barcodes Processed: "+rpstring+" \t"+String.format(Locale.ROOT, "%.2fk reads/sec", rpnano*1000000));
		outstream.println("Bases Processed:    "+bpstring+" \t"+String.format(Locale.ROOT, "%.2fm bases/sec", bpnano*1000));
		outstream.println();
		
		if(errorState){
			throw new RuntimeException("MergeBarcodes encountered an error; the output may be corrupt.");
		}
		
		FASTQ.FORCE_INTERLEAVED=oldForceInterleaved;
		FASTQ.TEST_INTERLEAVED=oldTestInterleaved;
		
		return map;
	}

	void mergeWithMap(Timer t, HashMap<String, Read> map){

		final ConcurrentReadInputStream cris;
		{
			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
			if(verbose){outstream.println("Started cris");}
			cris.start(); //4567
		}
		boolean paired=cris.paired();
		if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}

		final ConcurrentReadOutputStream ros;
		if(out1!=null){
			final int buff=4;

			if(cris.paired() && out2==null && (in1==null || !in1.contains(".sam"))){
				outstream.println("Writing interleaved.");
			}			

			assert(!out1.equalsIgnoreCase(in1) && !out1.equalsIgnoreCase(in1)) : "Input file and output file have same name.";
			assert(out2==null || (!out2.equalsIgnoreCase(in1) && !out2.equalsIgnoreCase(in2))) : "out1 and out2 have same name.";

			ros=ConcurrentReadOutputStream.getStream(ffout1, ffout2, qfout1, qfout2, buff, null, false);
			ros.start();
		}else{ros=null;}

		long readsProcessed=0;
		long basesProcessed=0;
		long barcodesFound=0;
		long barcodesNotFound=0;
		final StringBuilder prefix=new StringBuilder();

		{

			ListNum<Read> ln=cris.nextList();
			ArrayList<Read> reads=(ln!=null ? ln.list : null);

			//			outstream.println("Fetched "+reads);

			if(reads!=null && !reads.isEmpty()){
				Read r=reads.get(0);
				assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired());
			}

			while(reads!=null && reads.size()>0){

				for(int idx=0; idx<reads.size(); idx++){
					final Read r1=reads.get(idx);
					final Read r2=r1.mate;

					final int initialLength1=r1.length();
					final int initialLength2=(r1.mateLength());

					{
						readsProcessed++;
						basesProcessed+=initialLength1;
						if(reverseCompliment){r1.reverseComplement();}
					}
					if(r2!=null){
						readsProcessed++;
						basesProcessed+=initialLength2;
						if(reverseCompliment || reverseComplimentMate){r2.reverseComplement();}
					}

					String key=r1.id;
					if(key.indexOf(' ')>=0){key=key.split(" ")[0];}
					Read bar=map.remove(key);
					if(bar!=null){
						for(byte b : bar.bases){prefix.append((char)b);}
						prefix.append('_');
						for(byte b : bar.quality){prefix.append((char)(b+33));}
						prefix.append('_');
						r1.id=prefix+r1.id;
						barcodesFound++;
						if(r2!=null){
							r2.id=prefix+r2.id;
							barcodesFound++;
						}
						prefix.setLength(0);
					}else{
						barcodesNotFound++;
						if(r2!=null){barcodesNotFound++;}
					}
				}

				final ArrayList<Read> listOut=reads;

				if(ros!=null){ros.add(listOut, ln.id);}

				cris.returnList(ln.id, ln.list.isEmpty());
				ln=cris.nextList();
				reads=(ln!=null ? ln.list : null);
			}
			if(ln!=null){
				cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
			}
		}

		errorState|=ReadStats.writeAll();

		errorState|=ReadWrite.closeStreams(cris, ros);

		t.stop();

		double rpnano=readsProcessed/(double)(t.elapsed);
		double bpnano=basesProcessed/(double)(t.elapsed);

		String rpstring=(readsProcessed<100000 ? ""+readsProcessed : readsProcessed<100000000 ? (readsProcessed/1000)+"k" : (readsProcessed/1000000)+"m");
		String bpstring=(basesProcessed<100000 ? ""+basesProcessed : basesProcessed<100000000 ? (basesProcessed/1000)+"k" : (basesProcessed/1000000)+"m");

		while(rpstring.length()<8){rpstring=" "+rpstring;}
		while(bpstring.length()<8){bpstring=" "+bpstring;}

		{
			outstream.println("Barcodes Found:         \t"+barcodesFound+" reads ("+String.format(Locale.ROOT, "%.2f",barcodesFound*100.0/readsProcessed)+"%)");
			outstream.println("Barcodes Not Found:     \t"+barcodesNotFound+" reads ("+String.format(Locale.ROOT, "%.2f",barcodesNotFound*100.0/readsProcessed)+"%)");
		}

		outstream.println("Time:                         \t"+t);
		outstream.println("Reads Processed:    "+rpstring+" \t"+String.format(Locale.ROOT, "%.2fk reads/sec", rpnano*1000000));
		outstream.println("Bases Processed:    "+bpstring+" \t"+String.format(Locale.ROOT, "%.2fm bases/sec", bpnano*1000));

		if(errorState){
			throw new RuntimeException("ReformatReads terminated in an error state; the output may be corrupt.");
		}
	}
	
	/*--------------------------------------------------------------*/
	
	/** This is called if the program runs with no parameters */
	private void printOptions(){assert(false) : "Please read the associated shell script for usage information.";}
	
	/*--------------------------------------------------------------*/
	
	private String inbar=null;
	
	private String in1=null;
	private String in2=null;
	
	private String qfin1=null;
	private String qfin2=null;

	private String out1=null;
	private String out2=null;

	private String qfout1=null;
	private String qfout2=null;
	
	private String extin=null;
	private String extout=null;
	
	/*--------------------------------------------------------------*/

	private boolean reverseComplimentMate=false;
	private boolean reverseCompliment=false;
	/** Add /1 and /2 to read names */
	private boolean addslash=false;
	/** Add 1: and 2: to read names */
	private boolean addcolon=false;

	private long maxReads=-1;
	
	/*--------------------------------------------------------------*/
	
	private final FileFormat ffbar;
	
	private final FileFormat ffin1;
	private final FileFormat ffin2;

	private final FileFormat ffout1;
	private final FileFormat ffout2;
	
	
	/*--------------------------------------------------------------*/
	
	private PrintStream outstream=System.err;
	public static boolean verbose=false;
	public boolean errorState=false;
	private boolean overwrite=false;
	private boolean append=false;
	
}
