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package data.cerevisiae.region.zpeak;
import fork.lib.base.file.FileName;
import fork.lib.base.file.management.Dirs;
import fork.lib.bio.anno.genomic.BedGraphReader;
import fork.lib.bio.anno.genomic.LandscapeBuilder;
import fork.lib.bio.anno.genomic.PeakIdentifier;
import java.io.File;
/**
*
* @author forksapien
*/
public class GetPeaks {
public static void main(String[] args) throws Exception{ //debug
File dir= Dirs.getFile("dir");
File f= new File(dir+"/data/chip-seq/norm/norm_wig_chip_htz1-anti660_772-wt_sd_20131104-r1_pe1_sacCer1.wig");
File od= new File(dir+"/data/chip-seq/norm/peak3");
LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
PeakIdentifier pi= new PeakIdentifier(lb, null);
pi.getPeaks().writeToFileBed(new File(od+"/peak_"+FileName.getBaseName(f)+".bed"));
}
}