Package org.broadinstitute.gatk.utils

Examples of org.broadinstitute.gatk.utils.RandomDNA


    @DataProvider(name="trimmingData")
    public Iterator<Object[]> trimmingData() {
        final ActiveRegion activeRegion = new ActiveRegion(genomeLocParser.createGenomeLoc("chr1",1000,1100),genomeLocParser,25);
        final int length = activeRegion.getExtendedLoc().size();
        final RandomDNA rnd = new RandomDNA(13); // keep it prepoducible by fixing the seed to lucky 13.
        final ActiveRegionTestDataSet actd = new ActiveRegionTestDataSet(10,new String(rnd.nextBases(length)),new String[] {
                "Civar:*1T*" }, new String[0], new byte[0], new byte[0], new byte[0]);

        final List<Haplotype> haplotypes = actd.haplotypeList();
        for (final Haplotype h : haplotypes)
            h.setGenomeLocation(activeRegion.getExtendedLoc());
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