Examples with SVKmerShort org.broadinstitute.hellbender.tools.spark.sv.SVKmerShort used on opensource projects

Example 1 with SVKmerShort

use of org.broadinstitute.hellbender.tools.spark.sv.SVKmerShort in project gatk by broadinstitute.

the class ContainsKmerReadFilterTest method before.

@BeforeMethod
public void before() {
    final String kmerRef = "ATCGAGCGCTAGCGATGGCGCGCGATCGCGCTAGCGCGCTAGC";
    final SVKmerizer kmerizer = new SVKmerizer(kmerRef.getBytes(), kSize, new SVKmerShort(kSize));
    final ArrayList<SVKmer> kmerList = new ArrayList<>();
    while (kmerizer.hasNext()) {
        kmerList.add(kmerizer.next());
    }
    kmerSet = new HopscotchSet<>(kmerList);
}