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package hiseq;
import java.util.ArrayList;
import barcode.Barcode;
import barcode.BarcodeCounter;
import barcode.PCRMatrixHDist;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Parser;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import stream.ConcurrentReadInputStream;
import stream.ConcurrentReadOutputStream;
import stream.Read;
import structures.ByteBuilder;
import structures.ListNum;
/**
* @author Brian Bushnell
* @date Oct 6, 2014
*
*/
public class PlotReadPosition {
public static void main(String[] args){
//Start a timer immediately upon code entrance.
Timer t=new Timer();
//Create an instance of this class
PlotReadPosition x=new PlotReadPosition(args);
//Run the object
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
public PlotReadPosition(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
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;}
if(a.equals("expected") || a.equals("names") || a.equals("barcodes")){
expectedPath=b;
}else if(a.equals("parse_flag_goes_here")){
//Set a variable here
}else if(parser.parse(arg, a, b)){
//do nothing
}else{
// throw new RuntimeException("Unknown parameter "+args[i]);
assert(false) : "Unknown parameter "+args[i];
outstream.println("Unknown parameter "+args[i]);
}
}
{//Process parser fields
Parser.processQuality();
maxReads=parser.maxReads;
in1=parser.in1;
out1=parser.out1;
}
IlluminaHeaderParser1.PARSE_COMMENT=true;
ffout1=FileFormat.testOutput(out1, FileFormat.HEADER, ".header", true, true, false, false);
ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true);
final int delimiter=ffin1.barcodeDelimiter();
final int len1=ffin1.barcodeLength(1);
final int len2=ffin1.barcodeLength(2);
matrix=new PCRMatrixHDist(len1, len2, delimiter, true);
ArrayList<String> expected=BarcodeCounter.loadBarcodes(expectedPath, delimiter);
matrix.populateExpected(expected);
}
void process(Timer t){
final ConcurrentReadInputStream cris;
{
cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null);
cris.start();
}
boolean paired=cris.paired();
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, buff, "x\ty\thdist\n", false);
ros.start();
}else{ros=null;}
long readsProcessed=0, basesProcessed=0;
{
ListNum<Read> ln=cris.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
if(reads!=null && !reads.isEmpty()){
Read r=reads.get(0);
assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired());
}
ByteBuilder bb=new ByteBuilder(128);
while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
if(verbose){outstream.println("Fetched "+reads.size()+" reads.");}
for(int idx=0; idx<reads.size(); idx++){
final Read r1=reads.get(idx);
readsProcessed+=r1.pairCount();
basesProcessed+=r1.pairLength();
r1.mate=null;
// ********* Process reads here *********
ihp.parse(r1);
// System.err.println(ihp);
String barcode=ihp.barcode();
Barcode bc=matrix.findClosest(barcode, 99, 0);
int dist=barcode.length();
if(bc!=null) {
dist=bc.hdist(barcode);
}
bb.clear();
bb.append(ihp.xPos()).tab().append(ihp.yPos()).tab().append(dist);
r1.id=bb.toString();
}
if(ros!=null){ros.add(reads, ln.id);}
cris.returnList(ln);
if(verbose){outstream.println("Returned a list.");}
ln=cris.nextList();
reads=(ln!=null ? ln.list : null);
}
if(ln!=null){
cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
}
}
ReadWrite.closeStreams(cris, ros);
if(verbose){outstream.println("Finished.");}
t.stop();
outstream.println("Time: \t"+t);
outstream.println("Reads Processed: "+readsProcessed+" \t"+Tools.format("%.2fk reads/sec", (readsProcessed/(double)(t.elapsed))*1000000));
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
private String in1=null;
private String out1=null;
private String expectedPath=null;
private final FileFormat ffin1;
private final FileFormat ffout1;
/*--------------------------------------------------------------*/
private final PCRMatrixHDist matrix;
private final IlluminaHeaderParser2 ihp=new IlluminaHeaderParser2();
private long maxReads=-1;
/*--------------------------------------------------------------*/
private java.io.PrintStream outstream=System.err;
public static boolean verbose=false;
}
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