Examples with GERMLINE_DELETION com.hartwig.hmftools.bachelor.EligibilityReport.ReportType.GERMLINE_DELETION used on opensource projects

Example 1 with GERMLINE_DELETION

use of com.hartwig.hmftools.bachelor.EligibilityReport.ReportType.GERMLINE_DELETION in project hmftools by hartwigmedical.

the class BachelorEligibility method processCopyNumbers.

@NotNull
Collection<EligibilityReport> processCopyNumbers(final String patient, final List<GeneCopyNumber> copyNumbers) {
    final List<EligibilityReport> results = Lists.newArrayList();
    for (final GeneCopyNumber copyNumber : copyNumbers) {
        // TODO: verify the germline check
        final boolean isGermline = copyNumber.germlineHet2HomRegions() + copyNumber.germlineHomRegions() > 0;
        final List<String> matchingPrograms = programs.stream().filter(program -> program.copyNumberProcessor().test(copyNumber)).map(BachelorProgram::name).collect(Collectors.toList());
        final List<EligibilityReport> interimResults = matchingPrograms.stream().map(p -> ImmutableEligibilityReport.builder().patient(patient).source(isGermline ? GERMLINE_DELETION : SOMATIC_DELETION).program(p).id("").genes(copyNumber.gene()).chrom(copyNumber.chromosome()).pos(copyNumber.start()).ref("").alts("").effects("").build()).collect(Collectors.toList());
        results.addAll(interimResults);
    }
    return results;
}