Examples with SomaticVariantFactory com.hartwig.hmftools.common.variant.SomaticVariantFactory used on opensource projects

Example 1 with SomaticVariantFactory

use of com.hartwig.hmftools.common.variant.SomaticVariantFactory in project hmftools by hartwigmedical.

the class PurityPloidyEstimateApplication method somaticVariants.

@NotNull
private static List<SomaticVariant> somaticVariants(@NotNull final ConfigSupplier configSupplier) throws IOException {
    final SomaticConfig config = configSupplier.somaticConfig();
    if (config.file().isPresent()) {
        String filename = config.file().get().toString();
        LOGGER.info("Loading somatic variants from {}", filename);
        SomaticVariantFactory factory = SomaticVariantFactory.filteredInstance(new PassingVariantFilter(), new NTFilter(), new SGTFilter());
        return factory.fromVCFFile(configSupplier.commonConfig().tumorSample(), filename);
    } else {
        LOGGER.info("Somatic variants support disabled.");
        return Collections.emptyList();
    }
}