protected void init(){}
public void writeToDirectory(File od, String org) throws Exception{
GenomicRegionsModifier gm= new GenomicRegionsModifier(gb);
gm.gb.writeToFileBed(new File(od+"/"+org+"_gene_cds_full.bed"));
gm.getComplementaryStrand().writeToFileBed(new File(od+"/"+org+"_gene_cds-rev_full.bed"));
gm.getFivePrimeEnds(300, -150).writeToFileBed(new File(od+"/"+org+"_gene_five_300.-150.bed"));
gm.getFivePrimeEnds(150, 0).writeToFileBed(new File(od+"/"+org+"_gene_five_150.0.bed"));
gm.getFivePrimeEnds(0, 150).writeToFileBed(new File(od+"/"+org+"_gene_five_0.150.bed"));
gm.getFivePrimeEnds(-150, 300).writeToFileBed(new File(od+"/"+org+"_gene_five_-150.300.bed"));
new GenomicRegionsModifier(gm.getGenicRegions(300, 300)).lengthGreaterThan(100).writeToFileBed(new File(od+"/"+org+"_gene_cds_300.300.bed"));
gm.getThreePrimeEnds(300, -150).writeToFileBed(new File(od+"/"+org+"_gene_three_300.-150.bed"));
gm.getThreePrimeEnds(150, 0).writeToFileBed(new File(od+"/"+org+"_gene_three_150.0.bed"));
gm.getThreePrimeEnds(0, 150).writeToFileBed(new File(od+"/"+org+"_gene_three_0.150.bed"));
gm.getThreePrimeEnds(-150, 300).writeToFileBed(new File(od+"/"+org+"_gene_three_-150.300.bed"));
gm.getAllIntergenicRegions().writeToFileBed(new File(od+"/"+org+"_intergenic_full.bed"));
new GenomicRegionsModifier(gm.getAllIntergenicRegions()).getGenicRegions(300, 300) .writeToFileBed(new File(od+"/"+org+"_intergenic_300.bed"));
gm.getFivePrimeEnds(300, 0).writeToFileBed(new File(od+"/"+org+"_gene_five_300.0.bed"));
gm.getFivePrimeEnds(0, 300).writeToFileBed(new File(od+"/"+org+"_gene_five_0.300.bed"));
}