Examples with Program nl.hartwigmedicalfoundation.bachelor.Program used on opensource projects

Example 6 with Program

use of nl.hartwigmedicalfoundation.bachelor.Program in project hmftools by hartwigmedical.

the class BachelorSchema method processXML.

@Nullable
public Program processXML(final Path path) {
    LOGGER.info("loading input file: {}", path);
    try {
        final JAXBContext context = JAXBContext.newInstance(Program.class);
        final Unmarshaller unmarshaller = context.createUnmarshaller();
        unmarshaller.setSchema(schema);
        return (Program) unmarshaller.unmarshal(path.toFile());
    } catch (final JAXBException e) {
        LOGGER.error("failed to process: {}", path);
        LOGGER.error(e);
        return null;
    }
}

Example 7 with Program

use of nl.hartwigmedicalfoundation.bachelor.Program 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);
}