Examples with BachelorSchema com.hartwig.hmftools.bachelor.BachelorSchema used on opensource projects

Example 1 with BachelorSchema

use of com.hartwig.hmftools.bachelor.BachelorSchema in project hmftools by hartwigmedical.

the class BlacklistPredicateTest method setup.

@Before
public void setup() throws SAXException {
    BachelorSchema schema = BachelorSchema.make();
    final Program program = schema.processXML(Paths.get(BLACKLIST_XML));
    assertNotNull(program);
    blacklistPredicate = new BlacklistPredicate(Sets.newHashSet("ENST00000380152"), program.getBlacklist());
    VCFHeader header = new VCFHeader(Sets.newHashSet(), Sets.newHashSet(SAMPLE));
    codec = new VCFCodec();
    codec.setVCFHeader(header, VCFHeaderVersion.VCF4_2);
}