use of org.broadinstitute.hellbender.tools.spark.sv.SVKmerizer 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);
}
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