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package data.human.statham2014mods;
import fork.lib.base.file.FileName;
import fork.lib.base.file.management.Dirs;
import fork.lib.bio.anno.genomic.BedGraphReader;
import java.io.File;
/**
*
* @author man-mqbpjmg4
*/
public class GetPeaks {
public static void main(String[] args) throws Exception { //debug
File dir= Dirs.getFile("dir");
File d= new File(dir+"/other_datasets/statham2014_mcf7-mods/norm");
File od= new File(d+"/peaks");
File[] fs= d.listFiles();
for( int i=0; i<fs.length; i++ ){
File f= fs[i];
if(FileName.getExt(f).equals("wig")){
data.human.inhouse.chippeak.GetPeaks gg= new data.human.inhouse.chippeak.GetPeaks(new BedGraphReader(f).getLandscapeBuilder());
File out= new File(od+"/peak_"+FileName.getBaseName(f)+".bed");
gg.writeToFile(out);
}
}
}
}