Examples of BedReaderParam

Examples of fork.lib.bio.anno.genomic.BedReaderParam

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    //File f= new File(dir+"/anno/refGene_hg19.bed");String org= "hg19"; String tag= "refGene";
    File f= new File(dir+"/anno/ensGene_hg19_exon.bed");String org= "hg19"; String tag= "ensGene";
   
    File od= new File(dir+"/anno/bed/"+org+"/"+tag+"_"+org+"/genic");
   
    BedReaderParam par= new BedReaderParam();
    par.ifDirectional=true;
   
    GenomicRegionsBuilder gb= new BedReader(f, par).getGenomicRegionsBuilder();
   
    GenerateGenic gg= new GenerateGenic(gb);
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Examples of fork.lib.bio.anno.genomic.BedReaderParam

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    File f= new File(dir+"/anno/xu_2009_orfs.bed");String org= "sacCer1-xu";
   
   
    File od= new File(dir+"/anno/bed/"+org+"/200");
   
    BedReaderParam par= new BedReaderParam();
    par.ifDirectional=true;
   
    GenomicRegionsBuilder gb= new BedReader(f, par).getGenomicRegionsBuilder();
   
    Generate gg= new Generate(gb);
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Examples of fork.lib.bio.anno.genomic.BedReaderParam

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        this.f=f;
    }
   
   
public void writeToOutput(File out)throws Exception {
    BedReaderParam brp= new BedReaderParam();
    brp.ifReadExtension=true;
    GenomicRegionsBuilder gb= new BedReader(f, brp).getGenomicRegionsBuilder();
    GenomicRegionsBuilder gbout= new GenomicRegionsBuilder();
   
    Iterator<GenomicRegion> it= gb.iterator();
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Examples of fork.lib.bio.anno.genomic.BedReaderParam

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    //File f= new File(dir+"/anno/refGene_hg19.bed");String org= "refGene_hg19";
   
   
    File od= new File(dir+"/anno/bed/"+org);
   
    BedReaderParam par= new BedReaderParam();
    par.ifDirectional=true;
   
    GenomicRegionsBuilder gb= new BedReader(f, par).getGenomicRegionsBuilder();
   
    GenerateGenic gg= new GenerateGenic(gb);
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