Package fork.lib.bio.anno.genomic.region

Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsCrossover

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    }
   
   
   
public void writeToFile(File out)throws Exception {
    GenomicRegionsCrossover gc= new GenomicRegionsComparator(gb, gbcomp).getCrossover();
    HashSet<GenomicRegion> allrs= new HashSet<>();
    Iterator<GenomicRegion> it= gc.both.iterator();
    while(it.hasNext()){
        allrs.add( it.next() );
    }
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    GenomicRegionsBuilder gbc= new BedReader(reff).getGenomicRegionsBuilder();
   
    System.out.println(gbe.size());
    System.out.println(gbc.size());
   
    GenomicRegionsCrossover gc= new GenomicRegionsComparator(gbe, gbc).getCrossover();
    gc.print();

}
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    GenomicRegionsBuilder gbc= new BedReader(reff).getGenomicRegionsBuilder();
   
    System.out.println(gbe.size());
    System.out.println(gbc.size());
   
    GenomicRegionsCrossover gc= new GenomicRegionsComparator(gbe, gbc).getCrossover();
    gc.print();

}
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    random();
}


protected int ovl(GenomicRegionsBuilder tar, GenomicRegionsBuilder ref) throws Exception{
    GenomicRegionsCrossover gc=  new GenomicRegionsComparator(tar, ref).getCrossover();
    //gc.both.print();
    return gc.both.size();
    //return gc.tarOnly.size();
}
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public static GenomicRegionsBuilder overlap(GenomicRegionsBuilder tar, GenomicRegionsBuilder ref)throws Exception {
    GenomicRegionsCrossover gc= new GenomicRegionsComparator(tar, ref).getCrossover();
    return gc.both;
}
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    GenomicRegionsCrossover gc= new GenomicRegionsComparator(tar, ref).getCrossover();
    return gc.both;
}

public static GenomicRegionsBuilder tarOnly(GenomicRegionsBuilder tar, GenomicRegionsBuilder ref)throws Exception {
    GenomicRegionsCrossover gc= new GenomicRegionsComparator(tar, ref).getCrossover();
    return gc.tarOnly;
}
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Related Classes of fork.lib.bio.anno.genomic.region.GenomicRegionsCrossover

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