Examples with Exon com.github.lindenb.jvarkit.util.ucsc.KnownGene.Exon used on opensource projects

Example 1 with Exon

use of com.github.lindenb.jvarkit.util.ucsc.KnownGene.Exon in project jvarkit by lindenb.

the class FindNewSpliceSites method findJunction.

private boolean findJunction(Collection<KnownGene> genes, int start1, int end1) {
    for (final KnownGene g : genes) {
        for (int k = 0; k + 1 < g.getExonCount(); ++k) {
            final Exon ex0 = g.getExon(k);
            final Exon ex1 = g.getExon(k + 1);
            if (is_close_to(ex0.getEnd() + 1, start1) && is_close_to(ex1.getStart() + 1, end1)) {
                return true;
            }
        }
    }
    return false;
}