this.gb=gb;
}
public void writeToFile(File out)throws Exception{
GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
String[] chrs= gb.getChromosomeList();
for(int i=0; i<chrs.length ; i++){
String chr= chrs[i];
ArrayList<Region> rs= gb.getRegionsForChromosome(chr);
if(chr.equals("chr10")){
for(int j=0; j<rs.size() ; j++){
Region r= rs.get(j);
if(r.higherThan(117000d)){
r.setLowHigh(r.low-310, r.high-310);
gbout.add((GenomicRegion)r);
}else{
gbout.add((GenomicRegion)r);
}
}
}else{
gbout.addAll(chr, rs);
}
}
gbout.writeToFileBed(out);
}