package jgi;

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

import stream.ByteBuilder;
import stream.ConcurrentGenericReadInputStream;
import stream.ConcurrentReadInputStream;
import stream.FASTQ;
import stream.FastaReadInputStream;
import stream.ConcurrentReadOutputStream;
import stream.Read;
import align2.ListNum;
import align2.ReadStats;
import align2.Shared;
import align2.Tools;
import dna.Parser;
import dna.Timer;
import fileIO.ByteFile;
import fileIO.ByteFile1;
import fileIO.ByteFile2;
import fileIO.FileFormat;
import fileIO.ReadWrite;

/**
 * @author Brian Bushnell
 * @date Oct 17, 2014
 *
 */
public class A_Sample_Unpaired {
	
	public static void main(String[] args){
		Timer t=new Timer();
		A_Sample_Unpaired mb=new A_Sample_Unpaired(args);
		mb.process(t);
	}
	
	public A_Sample_Unpaired(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");

		
		
		Shared.READ_BUFFER_LENGTH=Tools.min(200, Shared.READ_BUFFER_LENGTH);
		Shared.capBuffers(4);
		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
		
		FASTQ.TEST_INTERLEAVED=FASTQ.FORCE_INTERLEAVED=false;
		
		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(parser.in1==null && i==0 && !arg.contains("=") && (arg.toLowerCase().startsWith("stdin") || new File(arg).exists())){
				parser.in1=arg;
			}else if(parser.out1==null && i==1 && !arg.contains("=")){
				parser.out1=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;
			
			in1=parser.in1;
			qfin1=parser.qfin1;

			out1=parser.out1;
			qfout1=parser.qfout1;
			
			extin=parser.extin;
			extout=parser.extout;
		}
		
		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){
			ByteFile.FORCE_MODE_BF2=false;
			ByteFile.FORCE_MODE_BF1=true;
		}

		if(out1!=null && out1.equalsIgnoreCase("null")){out1=null;}
		
		if(!Tools.testOutputFiles(overwrite, append, false, out1)){
			outstream.println((out1==null)+", "+out1);
			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+"\n");
		}
		
		ffout1=FileFormat.testOutput(out1, FileFormat.FASTQ, extout, true, overwrite, append, false);

		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
	}
	
	void process(Timer t){
		
		final ConcurrentReadInputStream cris;
		{
			cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null);
			cris.start();
			if(verbose){outstream.println("Started cris");}
		}
		boolean paired=cris.paired();
//		if(verbose){
			if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
//		}

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

			assert(!out1.equalsIgnoreCase(in1) && !out1.equalsIgnoreCase(in1)) : "Input file and output file have same name.";
			
			ros=ConcurrentReadOutputStream.getStream(ffout1, null, qfout1, null, buff, null, false);
			ros.start();
		}else{ros=null;}
		
		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((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 int initialLength1=r1.length();
					
					readsProcessed++;
					basesProcessed+=initialLength1;
				}
				
				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("Time:                         \t"+t);
		outstream.println("Reads Processed:    "+rpstring+" \t"+String.format("%.2fk reads/sec", rpnano*1000000));
		outstream.println("Bases Processed:    "+bpstring+" \t"+String.format("%.2fm bases/sec", bpnano*1000));
		
		if(errorState){
			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
		}
	}
	
	/*--------------------------------------------------------------*/
	
	private void printOptions(){
		assert(false) : "printOptions: TODO";
//		outstream.println("Syntax:\n");
//		outstream.println("java -ea -Xmx512m -cp <path> jgi.ReformatReads in=<infile> in2=<infile2> out=<outfile> out2=<outfile2>");
//		outstream.println("\nin2 and out2 are optional.  \nIf input is paired and there is only one output file, it will be written interleaved.\n");
//		outstream.println("Other parameters and their defaults:\n");
//		outstream.println("overwrite=false  \tOverwrites files that already exist");
//		outstream.println("ziplevel=4       \tSet compression level, 1 (low) to 9 (max)");
//		outstream.println("interleaved=false\tDetermines whether input file is considered interleaved");
//		outstream.println("fastawrap=70     \tLength of lines in fasta output");
//		outstream.println("qin=auto         \tASCII offset for input quality.  May be set to 33 (Sanger), 64 (Illumina), or auto");
//		outstream.println("qout=auto        \tASCII offset for output quality.  May be set to 33 (Sanger), 64 (Illumina), or auto (meaning same as input)");
//		outstream.println("outsingle=<file> \t(outs) Write singleton reads here, when conditionally discarding reads from pairs.");
	}
	
	
	/*--------------------------------------------------------------*/
	
	private String in1=null;
	
	private String qfin1=null;

	private String out1=null;

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

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

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