Examples of org.broadinstitute.gatk.utils.haplotype.Haplotype.trim()

Package org.broadinstitute.gatk.utils.haplotype

Class org.broadinstitute.gatk.utils.haplotype.Haplotype

Examples of org.broadinstitute.gatk.utils.haplotype.Haplotype.trim()

org.broadinstitute.gatk.utils.haplotype.Haplotype.trim()
Create a new Haplotype derived from this one that exactly spans the provided location Note that this haplotype must have a contain a genome loc for this operation to be successful. If no GenomeLoc is contained than @throws an IllegalStateException Also loc must be fully contained within this Haplotype's genomeLoc. If not an IllegalArgumentException is thrown. @param loc a location completely contained within this Haplotype's location @return a new Haplotype within only the bases spanning the provided location, or null for some reason the haplotype would be malformed if


    @Test(expectedExceptions = IllegalArgumentException.class)
    public void testBadTrimLoc() {
        final GenomeLoc loc = new UnvalidatingGenomeLoc("20", 0, 10, 20);
        final Haplotype hap = new Haplotype("ACGTAACCGGT".getBytes(), loc);
        hap.trim(new UnvalidatingGenomeLoc("20", 0, 1, 20));
    }


    @Test(expectedExceptions = IllegalStateException.class)
    public void testBadTrimNoLoc() {
        final Haplotype hap = new Haplotype("ACGTAACCGGT".getBytes());

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    }


    @Test(expectedExceptions = IllegalStateException.class)
    public void testBadTrimNoLoc() {
        final Haplotype hap = new Haplotype("ACGTAACCGGT".getBytes());
        hap.trim(new UnvalidatingGenomeLoc("20", 0, 1, 20));
    }
}

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