package org.seqcode.deepseq.utils;

import java.io.FileWriter;

import java.io.IOException;

import java.sql.SQLException;

import java.util.List;

import org.seqcode.deepseq.StrandedBaseCount;

import org.seqcode.deepseq.experiments.ControlledExperiment;

import org.seqcode.deepseq.experiments.ExperimentCondition;

import org.seqcode.deepseq.experiments.ExperimentManager;

import org.seqcode.deepseq.experiments.ExptConfig;

import org.seqcode.genome.GenomeConfig;

import org.seqcode.genome.location.NamedRegion;

import org.seqcode.genome.location.Region;

import org.seqcode.gsebricks.verbs.location.ChromRegionIterator;

import org.seqcode.gseutils.Args;

import org.seqcode.gseutils.NotFoundException;

public class BEDExporter {

protected GenomeConfig gconfig;

protected ExptConfig econfig;

protected ExperimentManager manager;

protected int [] stackedHitCountsPos;

protected int [] stackedHitCountsNeg;

final int MAXSECTION=50000000;

private int readLength=1;

private String outName="out";

public static void main(String[] args) throws SQLException, NotFoundException {

GenomeConfig gconfig = new GenomeConfig(args);

ExptConfig econfig = new ExptConfig(gconfig.getGenome(), args);

if(args.length==0 || gconfig.helpWanted()){

System.err.println("BEDExporter usage:\n" +

GenomeConfig.getArgsList()+"\n"+

ExptConfig.getArgsList()+"n"+

"BEDExporter:\n"+

"\t--readlen <read length>\n" +

"\t--out <output file name>");

System.exit(1);

}else{

String outName = Args.parseString(args,"out","out");

int readLen = Args.parseInteger(args,"readlen",40);

BEDExporter exporter = new BEDExporter(gconfig, econfig, outName, readLen);

exporter.execute();

exporter.close();

}

}

public BEDExporter(GenomeConfig gcon, ExptConfig econ, String out, int rL) {

gconfig = gcon;

econfig = econ;

manager = new ExperimentManager(econfig);

readLength = rL;

}

public void execute(){

for(ExperimentCondition c : manager.getConditions()){

for(ControlledExperiment rep : c.getReplicates()){

System.err.println("Condition "+c.getName()+":\tRep "+rep.getName());

try {

FileWriter fw = new FileWriter(outName+"."+c.getName()+"."+rep.getName()+".bed");

//fw.write("chrom\tindex\tforward\treverse\tvalue\n");

double basesDone=0, printStep=10000000, numPrint=0;

ChromRegionIterator chroms = new ChromRegionIterator(gconfig.getGenome());

while(chroms.hasNext()){

NamedRegion currentRegion = chroms.next();

//Split the job up into chunks of 100Mbp

for(int x=currentRegion.getStart(); x<=currentRegion.getEnd(); x+=100000000){

int y = x+100000000;

if(y>currentRegion.getEnd()){y=currentRegion.getEnd();}

Region currSubRegion = new Region(gconfig.getGenome(), currentRegion.getChrom(), x, y);

List<StrandedBaseCount> hits = rep.getSignal().getBases(currSubRegion);

double stackedHitCountsPos[] = make5PrimeLandscape(hits, currSubRegion, '+');

double stackedHitCountsNeg[] = make5PrimeLandscape(hits, currSubRegion, '-');

//Scan regions

for(int i=currSubRegion.getStart(); i<currSubRegion.getEnd(); i++){

int offset = i-currSubRegion.getStart();

double posHits=stackedHitCountsPos[offset];

double negHits=stackedHitCountsNeg[offset];

if(posHits>0 || negHits>0){

for(int hitc=0; hitc<(int)posHits; hitc++){

fw.write("chr"+currSubRegion.getChrom()+"\t"+i+"\t"+(i+readLength)+"\t"+"+"+"\n");

}

for(int hitc=0; hitc<(int)negHits; hitc++){

fw.write("chr"+currSubRegion.getChrom()+"\t"+(i+1-readLength)+"\t"+(i+1)+"\t"+"-"+"\n");

}

}

//Print out progress

basesDone++;

if(basesDone > numPrint*printStep){

if(numPrint%10==0){System.out.print(String.format("(%.0f)", (numPrint*printStep)));}

else{System.out.print(".");}

if(numPrint%50==0 && numPrint!=0){System.out.print("\n");}

numPrint++;

}

}

}

}

System.out.print("\n");

fw.close();

} catch (IOException e) {

e.printStackTrace();

}

}

}

}

public void close(){

manager.close();

}

protected double[] make5PrimeLandscape(List<StrandedBaseCount> hits, Region currReg, char strand){

double[] startcounts = new double[(int)currReg.getWidth()+1];

for(int i=0; i<=currReg.getWidth(); i++){startcounts[i]=0;}

for(StrandedBaseCount r : hits){

if(strand=='.' || r.getStrand()==strand){

if(r.getCoordinate()>=currReg.getStart() && r.getCoordinate()<=currReg.getEnd()){

int offset5=inBounds(r.getCoordinate()-currReg.getStart(),0,currReg.getWidth());

startcounts[offset5]+=r.getCount();

}

}

}

return(startcounts);

}

//keep the number in bounds

protected final double inBounds(double x, double min, double max){

if(x<min){return min;}

if(x>max){return max;}

return x;

}

protected final int inBounds(int x, int min, int max){

if(x<min){return min;}

if(x>max){return max;}

return x;

}

}