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

Example 11 with StructuralVariant

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

the class StructuralVariantLegsFactory method create.

@NotNull
static List<StructuralVariantLegs> create(@NotNull final List<StructuralVariant> variants) {
    final List<ModifiableStructuralVariantLegs> result = createLegs(false, variants);
    final Multimap<GenomePosition, ModifiableStructuralVariantLegs> duplicates = findDuplicates(result);
    for (GenomePosition duplicatePosition : duplicates.keySet()) {
        final StructuralVariantLeg approvedLeg = reduce(duplicatePosition, duplicates.get(duplicatePosition));
        boolean match = false;
        for (ModifiableStructuralVariantLegs legs : duplicates.get(duplicatePosition)) {
            Optional<StructuralVariantLeg> start = legs.start();
            if (start.filter(x -> isDuplicate(duplicatePosition, x)).isPresent()) {
                assert start.isPresent();
                if (start.get().equals(approvedLeg)) {
                    match = true;
                } else {
                    legs.setStart(Optional.empty());
                }
            }
            Optional<StructuralVariantLeg> end = legs.end();
            if (end.filter(x -> isDuplicate(duplicatePosition, x)).isPresent()) {
                assert end.isPresent();
                if (end.get().equals(approvedLeg)) {
                    match = true;
                } else {
                    legs.setEnd(Optional.empty());
                }
            }
        }
        if (!match) {
            result.add(ModifiableStructuralVariantLegs.create().setStart(approvedLeg).setEnd(Optional.empty()));
        }
    }
    return new ArrayList<>(result);
}

Example 12 with StructuralVariant

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

the class PatientReporter method analyseGenomeData.

@NotNull
private GenomeAnalysis analyseGenomeData(@NotNull final String sample, @NotNull final String runDirectory) throws IOException {
    LOGGER.info(" Loading somatic snv and indels...");
    final List<SomaticVariant> variants = PatientReporterHelper.loadPassedSomaticVariants(sample, runDirectory);
    LOGGER.info("  " + variants.size() + " somatic passed snps, mnps and indels loaded for sample " + sample);
    LOGGER.info(" Analyzing somatic snp/mnp and indels....");
    final VariantAnalysis variantAnalysis = variantAnalyzer().run(variants);
    LOGGER.info(" Loading purity numbers...");
    final PurityContext context = PatientReporterHelper.loadPurity(runDirectory, sample);
    if (context.status().equals(FittedPurityStatus.NO_TUMOR)) {
        LOGGER.warn("PURPLE DID NOT DETECT A TUMOR. Proceed with utmost caution!");
    }
    final FittedPurity purity = context.bestFit();
    final FittedPurityScore purityScore = context.score();
    final List<PurpleCopyNumber> purpleCopyNumbers = PatientReporterHelper.loadPurpleCopyNumbers(runDirectory, sample);
    final List<GeneCopyNumber> panelGeneCopyNumbers = PatientReporterHelper.loadPurpleGeneCopyNumbers(runDirectory, sample).stream().filter(x -> reporterData().panelGeneModel().panel().contains(x.gene())).collect(Collectors.toList());
    LOGGER.info("  " + purpleCopyNumbers.size() + " purple copy number regions loaded for sample " + sample);
    LOGGER.info(" Analyzing purple somatic copy numbers...");
    final PurpleAnalysis purpleAnalysis = ImmutablePurpleAnalysis.builder().gender(context.gender()).status(context.status()).fittedPurity(purity).fittedScorePurity(purityScore).copyNumbers(purpleCopyNumbers).panelGeneCopyNumbers(panelGeneCopyNumbers).build();
    final Path structuralVariantVCF = PatientReporterHelper.findStructuralVariantVCF(runDirectory);
    LOGGER.info(" Loading structural variants...");
    final List<StructuralVariant> structuralVariants = StructuralVariantFileLoader.fromFile(structuralVariantVCF.toString(), true);
    LOGGER.info(" Enriching structural variants with purple data.");
    final List<EnrichedStructuralVariant> enrichedStructuralVariants = purpleAnalysis.enrichStructuralVariants(structuralVariants);
    LOGGER.info(" Analysing structural variants...");
    final StructuralVariantAnalysis structuralVariantAnalysis = structuralVariantAnalyzer().run(enrichedStructuralVariants, false);
    return ImmutableGenomeAnalysis.of(sample, variantAnalysis, purpleAnalysis, structuralVariantAnalysis);
}

Example 13 with StructuralVariant

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

the class SvVCFAnnotator method generateFilteredSVFile.

private void generateFilteredSVFile(final List<StructuralVariant> variants, final String sampleId) {
    try {
        if (mFileWriter == null) {
            String outputFileName = mOutputPath;
            if (!outputFileName.endsWith("/"))
                outputFileName += "/";
            outputFileName += "svs_incl_filtered.csv";
            Path outputFile = Paths.get(outputFileName);
            mFileWriter = Files.newBufferedWriter(outputFile);
            mFileWriter.write("SampleId,SvId,Type,ChrStart,PosStart,OrientStart,ChrEnd,PosEnd,OrientEnd,Filters\n");
        }
        for (final StructuralVariant var : variants) {
            String filtersStr = var.filters();
            if (filtersStr.equals("PASS") || filtersStr.equals("[]") || filtersStr.isEmpty()) {
                LOGGER.debug("var({}) was a PASS", var.id());
                filtersStr = "PASS";
            } else {
                // make tokenisable for further searches
                LOGGER.debug("var({}) has filters: {}", var.id(), var.filters());
                if (filtersStr.charAt(0) == '[')
                    filtersStr = filtersStr.substring(1);
                if (filtersStr.charAt(filtersStr.length() - 1) == ']')
                    filtersStr = filtersStr.substring(0, filtersStr.length() - 1);
                if (!filtersStr.isEmpty())
                    filtersStr = filtersStr.replace(",", ";");
            }
            mFileWriter.write(String.format("%s,%s,%s,%s,%d,%d,%s,%d,%d,%s", sampleId, var.id(), var.type(), var.chromosome(true), var.position(true), var.orientation(true), var.chromosome(false), var.position(false), var.orientation(false), filtersStr));
            mFileWriter.newLine();
        }
    } catch (final IOException e) {
        LOGGER.error("error writing to outputFile");
    }
}

Example 14 with StructuralVariant

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

the class StructuralVariantLegsFactoryTest method testSameVAF.

@Test
public void testSameVAF() {
    final StructuralVariant first = sv(100, 200, StructuralVariantType.INV, 0.25, 0.25);
    final StructuralVariant second = sv(200, 300, StructuralVariantType.BND, 0.25, 0.25);
    final List<StructuralVariant> variants = Lists.newArrayList(first, second);
    final List<StructuralVariantLegs> legs = StructuralVariantLegsFactory.create(variants);
    assertEquals(2, legs.size());
    assertTrue(legs.get(0).start().isPresent());
    assertTrue(legs.get(0).end().isPresent());
    assertTrue(legs.get(1).start().isPresent());
    assertTrue(legs.get(1).end().isPresent());
    assertLeg(1, 0.25, legs.get(0).start().get());
    assertLeg(1, 0.25, legs.get(0).end().get());
    assertLeg(1, 0.25, legs.get(1).start().get());
    assertLeg(1, 0.25, legs.get(1).end().get());
}

Example 15 with StructuralVariant

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

the class StructuralVariantPositionFactoryTest method excludeInserts.

@Test
public void excludeInserts() {
    final StructuralVariant variant = PurpleDatamodelTest.createStructuralVariant("1", 1001, "1", 1001, StructuralVariantType.INS).build();
    assertEquals(0, ClusterVariantLegFactory.create(Lists.newArrayList(variant)).size());
}