Examples with Range org.apache.commons.lang3.Range used on opensource projects

Example 6 with Range

use of org.apache.commons.lang3.Range in project hmftools by hartwigmedical.

the class Analysis method processStructuralVariant.

StructuralVariantResult processStructuralVariant(final HMFVariantContext ctx) throws IOException {
    final QueryInterval[] intervals = QueryInterval.optimizeIntervals(new QueryInterval[] { new QueryInterval(ctx.MantaBP1.ReferenceIndex, Math.max(0, ctx.MantaBP1.Position + ctx.Uncertainty1.Start - range), ctx.MantaBP1.Position + ctx.Uncertainty1.End + range), new QueryInterval(ctx.MantaBP2.ReferenceIndex, Math.max(0, ctx.MantaBP2.Position + ctx.Uncertainty2.Start - range), ctx.MantaBP2.Position + ctx.Uncertainty2.End + range) });
    final File TEMP_REF_BAM = queryNameSortedBAM(refReader, intervals, "ref");
    final File TEMP_TUMOR_BAM = queryNameSortedBAM(tumorReader, intervals, "tumor");
    final SamReader SORTED_REF_READER = SamReaderFactory.makeDefault().open(TEMP_REF_BAM);
    final SamReader SORTED_TUMOR_READER = SamReaderFactory.makeDefault().open(TEMP_TUMOR_BAM);
    final BreakpointResult breakpoints = determineBreakpoints(ctx, SORTED_TUMOR_READER);
    final StructuralVariantResult result = new StructuralVariantResult();
    result.Breakpoints = breakpoints.Breakpoints;
    result.QueryIntervals = intervals;
    if (breakpoints.Error != BreakpointError.NONE) {
        result.Filters = Filter.getErrorFilter();
    } else {
        result.TumorStats = collectEvidence(ctx, SORTED_TUMOR_READER, result.Breakpoints);
        result.RefStats = collectEvidence(ctx, SORTED_REF_READER, result.Breakpoints);
        result.AlleleFrequency = AlleleFrequency.calculate(result.TumorStats);
        // load sample clipping
        SORTED_TUMOR_READER.forEach(r -> Clipping.getClips(r).forEach(c -> result.TumorStats.Sample_Clipping.add(c)));
        SORTED_REF_READER.forEach(r -> Clipping.getClips(r).forEach(c -> result.RefStats.Sample_Clipping.add(c)));
        result.Filters = Filter.getFilters(ctx, result.TumorStats, result.RefStats, result.Breakpoints, contamination);
        // adjust for homology
        final Location bp1 = result.Breakpoints.getLeft().add(ctx.OrientationBP1 > 0 ? 0 : -1);
        final Location bp2;
        if (!ctx.isInsert() && ctx.InsertSequence.isEmpty()) {
            bp2 = result.Breakpoints.getRight().add(-ctx.OrientationBP2 * ctx.HomologySequence.length()).add(ctx.OrientationBP2 > 0 ? 0 : -1);
        } else {
            bp2 = result.Breakpoints.getRight().add(ctx.OrientationBP2 > 0 ? 0 : -1);
        }
        result.Breakpoints = Pair.of(bp1, bp2);
    }
    result.FilterString = result.Filters.isEmpty() ? "PASS" : String.join(";", result.Filters);
    // clean up
    SORTED_REF_READER.close();
    SORTED_TUMOR_READER.close();
    if (!TEMP_REF_BAM.delete()) {
        LOGGER.error("couldn't delete {}", TEMP_REF_BAM);
    }
    if (!TEMP_TUMOR_BAM.delete()) {
        LOGGER.error("couldn't delete {}", TEMP_TUMOR_BAM);
    }
    return result;
}

Example 7 with Range

use of org.apache.commons.lang3.Range in project hmftools by hartwigmedical.

the class BreakPointInspectorApplication method main.

public static void main(final String... args) throws IOException {
    final AnalysisBuilder analysisBuilder = new AnalysisBuilder();
    final Options options = createOptions();
    try {
        final CommandLine cmd = createCommandLine(options, args);
        final String refPath = cmd.getOptionValue(REF_PATH);
        final String refSlicePath = cmd.getOptionValue(REF_SLICE);
        final String tumorPath = cmd.getOptionValue(TUMOR_PATH);
        final String tumorSlicePath = cmd.getOptionValue(TUMOR_SLICE);
        final String vcfPath = cmd.getOptionValue(VCF);
        if (cmd.hasOption(PROXIMITY)) {
            analysisBuilder.setRange(Integer.parseInt(cmd.getOptionValue(PROXIMITY, "500")));
        }
        if (cmd.hasOption(CONTAMINATION)) {
            analysisBuilder.setContaminationFraction(Float.parseFloat(cmd.getOptionValue(CONTAMINATION, "0")));
        }
        if (refPath == null || tumorPath == null || vcfPath == null) {
            printHelpAndExit(options);
            return;
        }
        final File tumorBAM = new File(tumorPath);
        final SamReader tumorReader = SamReaderFactory.makeDefault().open(tumorBAM);
        final File refBAM = new File(refPath);
        final SamReader refReader = SamReaderFactory.makeDefault().open(refBAM);
        final File vcfFile = new File(vcfPath);
        final VCFFileReader vcfReader = new VCFFileReader(vcfFile, false);
        final List<String> samples = vcfReader.getFileHeader().getGenotypeSamples();
        if (samples.size() != 2) {
            System.err.println("could not determine tumor and sample from VCF");
            System.exit(1);
            return;
        }
        TSVOutput.PrintHeaders();
        final Analysis analysis = analysisBuilder.setRefReader(refReader).setTumorReader(tumorReader).createAnalysis();
        final List<QueryInterval> combinedQueryIntervals = Lists.newArrayList();
        final Map<String, VariantContext> variantMap = new HashMap<>();
        final List<VariantContext> variants = Lists.newArrayList();
        for (VariantContext variant : vcfReader) {
            variantMap.put(variant.getID(), variant);
            final VariantContext mateVariant = variant;
            if (variant.hasAttribute("MATEID")) {
                variant = variantMap.get(variant.getAttributeAsString("MATEID", ""));
                if (variant == null) {
                    continue;
                }
            }
            final String location = variant.getContig() + ":" + Integer.toString(variant.getStart());
            final Location location1 = Location.parseLocationString(location, tumorReader.getFileHeader().getSequenceDictionary());
            final Range uncertainty1 = extractCIPOS(variant);
            final List<Integer> CIEND = variant.getAttributeAsIntList("CIEND", 0);
            Range uncertainty2 = CIEND.size() == 2 ? new Range(CIEND.get(0), CIEND.get(1)) : null;
            final boolean IMPRECISE = variant.hasAttribute("IMPRECISE");
            HMFVariantType svType;
            final Location location2;
            switch(variant.getStructuralVariantType()) {
                case INS:
                    svType = HMFVariantType.INS;
                    location2 = location1.set(variant.getAttributeAsInt("END", 0));
                    break;
                case INV:
                    if (variant.hasAttribute("INV3")) {
                        svType = HMFVariantType.INV3;
                    } else if (variant.hasAttribute("INV5")) {
                        svType = HMFVariantType.INV5;
                    } else {
                        System.err.println(variant.getID() + " : expected either INV3 or INV5 flag");
                        continue;
                    }
                    location2 = location1.add(Math.abs(variant.getAttributeAsInt("SVLEN", 0)));
                    break;
                case DEL:
                    svType = HMFVariantType.DEL;
                    location2 = location1.add(Math.abs(variant.getAttributeAsInt("SVLEN", 0)));
                    break;
                case DUP:
                    svType = HMFVariantType.DUP;
                    location2 = location1.add(Math.abs(variant.getAttributeAsInt("SVLEN", 0)));
                    break;
                case BND:
                    // process the breakend string
                    final String call = variant.getAlternateAllele(0).getDisplayString();
                    final String[] leftSplit = call.split("\\]");
                    final String[] rightSplit = call.split("\\[");
                    if (leftSplit.length >= 2) {
                        location2 = Location.parseLocationString(leftSplit[1], tumorReader.getFileHeader().getSequenceDictionary());
                        if (leftSplit[0].length() > 0) {
                            svType = HMFVariantType.INV3;
                            uncertainty2 = Range.invert(uncertainty1);
                        } else {
                            svType = HMFVariantType.DUP;
                            uncertainty2 = uncertainty1;
                        }
                    } else if (rightSplit.length >= 2) {
                        location2 = Location.parseLocationString(rightSplit[1], tumorReader.getFileHeader().getSequenceDictionary());
                        if (rightSplit[0].length() > 0) {
                            svType = HMFVariantType.DEL;
                            uncertainty2 = uncertainty1;
                        } else {
                            svType = HMFVariantType.INV5;
                            uncertainty2 = Range.invert(uncertainty1);
                        }
                    } else {
                        System.err.println(variant.getID() + " : could not parse breakpoint");
                        continue;
                    }
                    if (IMPRECISE) {
                        uncertainty2 = extractCIPOS(mateVariant);
                    }
                    break;
                default:
                    System.err.println(variant.getID() + " : UNEXPECTED SVTYPE=" + variant.getStructuralVariantType());
                    continue;
            }
            final HMFVariantContext ctx = new HMFVariantContext(variant.getID(), location1, location2, svType, IMPRECISE);
            ctx.Filter.addAll(variant.getFilters().stream().filter(s -> !s.startsWith("BPI")).collect(Collectors.toSet()));
            ctx.Uncertainty1 = uncertainty1;
            ctx.Uncertainty2 = ObjectUtils.firstNonNull(uncertainty2, fixup(uncertainty1, IMPRECISE, svType == HMFVariantType.INV3 || svType == HMFVariantType.INV5));
            ctx.HomologySequence = variant.getAttributeAsString("HOMSEQ", "");
            if (variant.hasAttribute("LEFT_SVINSSEQ") && variant.hasAttribute("RIGHT_SVINSSEQ")) {
                ctx.InsertSequence = variant.getAttributeAsString("LEFT_SVINSSEQ", "") + "..." + variant.getAttributeAsString("RIGHT_SVINSSEQ", "");
            } else {
                ctx.InsertSequence = variant.getAttributeAsString("SVINSSEQ", "");
            }
            ctx.BND = variant.getStructuralVariantType() == StructuralVariantType.BND;
            switch(ctx.Type) {
                case INS:
                case DEL:
                    ctx.OrientationBP1 = 1;
                    ctx.OrientationBP2 = -1;
                    break;
                case INV3:
                    ctx.OrientationBP1 = 1;
                    ctx.OrientationBP2 = 1;
                    break;
                case INV5:
                    ctx.OrientationBP1 = -1;
                    ctx.OrientationBP2 = -1;
                    break;
                case DUP:
                    ctx.OrientationBP1 = -1;
                    ctx.OrientationBP2 = 1;
                    break;
            }
            final StructuralVariantResult result = analysis.processStructuralVariant(ctx);
            combinedQueryIntervals.addAll(asList(result.QueryIntervals));
            TSVOutput.print(variant, ctx, result);
            final BiConsumer<VariantContext, Boolean> vcfUpdater = (v, swap) -> {
                final Set<String> filters = v.getCommonInfo().getFiltersMaybeNull();
                if (filters != null) {
                    filters.clear();
                }
                // we will map BreakpointError to a flag
                if (result.Filters.contains(Filter.Filters.BreakpointError.toString())) {
                    v.getCommonInfo().putAttribute("BPI_AMBIGUOUS", true, true);
                } else {
                    v.getCommonInfo().addFilters(result.Filters);
                }
                if (result.Filters.isEmpty()) {
                    final List<Double> af = asList(result.AlleleFrequency.getLeft(), result.AlleleFrequency.getRight());
                    v.getCommonInfo().putAttribute(AlleleFrequency.VCF_INFO_TAG, swap ? Lists.reverse(af) : af, true);
                }
                if (result.Breakpoints.getLeft() != null) {
                    v.getCommonInfo().putAttribute(swap ? "BPI_END" : "BPI_START", result.Breakpoints.getLeft().Position, true);
                }
                if (result.Breakpoints.getRight() != null) {
                    v.getCommonInfo().putAttribute(swap ? "BPI_START" : "BPI_END", result.Breakpoints.getRight().Position, true);
                }
                // remove CIPOS / CIEND when we have an insert sequence
                if (!v.hasAttribute("IMPRECISE") && v.hasAttribute("SVINSSEQ")) {
                    v.getCommonInfo().removeAttribute("CIPOS");
                    v.getCommonInfo().removeAttribute("CIEND");
                }
                variants.add(v);
            };
            vcfUpdater.accept(variant, false);
            if (mateVariant != variant) {
                vcfUpdater.accept(mateVariant, true);
            }
        }
        // TODO: update START, END with BPI values and save Manta values in new attributes
        final String vcfOutputPath = cmd.getOptionValue(VCF_OUT);
        if (vcfOutputPath != null) {
            final VCFHeader header = vcfReader.getFileHeader();
            header.addMetaDataLine(new VCFInfoHeaderLine("BPI_START", 1, VCFHeaderLineType.Integer, "BPI adjusted breakend location"));
            header.addMetaDataLine(new VCFInfoHeaderLine("BPI_END", 1, VCFHeaderLineType.Integer, "BPI adjusted breakend location"));
            header.addMetaDataLine(new VCFInfoHeaderLine("BPI_AMBIGUOUS", 0, VCFHeaderLineType.Flag, "BPI could not determine the breakpoints, inspect manually"));
            header.addMetaDataLine(new VCFHeaderLine("bpiVersion", BreakPointInspectorApplication.class.getPackage().getImplementationVersion()));
            Filter.UpdateVCFHeader(header);
            AlleleFrequency.UpdateVCFHeader(header);
            // setup VCF
            final VariantContextWriter writer = new VariantContextWriterBuilder().setReferenceDictionary(header.getSequenceDictionary()).setOutputFile(vcfOutputPath).build();
            writer.writeHeader(header);
            // write variants
            variants.sort(new VariantContextComparator(header.getSequenceDictionary()));
            variants.forEach(writer::add);
            writer.close();
        }
        final QueryInterval[] optimizedIntervals = QueryInterval.optimizeIntervals(combinedQueryIntervals.toArray(new QueryInterval[combinedQueryIntervals.size()]));
        if (tumorSlicePath != null) {
            writeToSlice(tumorSlicePath, tumorReader, optimizedIntervals);
        }
        if (refSlicePath != null) {
            writeToSlice(refSlicePath, refReader, optimizedIntervals);
        }
        refReader.close();
        tumorReader.close();
    } catch (ParseException e) {
        printHelpAndExit(options);
        System.exit(1);
    }
}

Example 8 with Range

use of org.apache.commons.lang3.Range in project incubator-gobblin by apache.

the class SalesforceSource method getHistogramByProbing.

/**
 * Get a histogram for the time range by probing to break down large buckets. Use count instead of
 * querying if it is non-negative.
 */
private Histogram getHistogramByProbing(TableCountProbingContext probingContext, int count, long startEpoch, long endEpoch) {
    Histogram histogram = new Histogram();
    Map<String, String> values = new HashMap<>();
    values.put("table", probingContext.entity);
    values.put("column", probingContext.watermarkColumn);
    values.put("greater", ">=");
    values.put("less", "<");
    StrSubstitutor sub = new StrSubstitutor(values);
    getHistogramRecursively(probingContext, histogram, sub, values, count, startEpoch, endEpoch);
    return histogram;
}

Example 9 with Range

use of org.apache.commons.lang3.Range in project webanno by webanno.

the class TypeSystemAnalysis method analyzeRelationLayer.

private Optional<RelationDetails> analyzeRelationLayer(TypeSystem aTS, Type aType) {
    // A UIMA type can be a relation layer if...
    // ... there are exactly two non-primitive features
    // ... both have the same range
    // ... the range is a span layer
    List<Feature> nonPrimitiveFeatures = aType.getFeatures().stream().filter(f -> !isBuiltInFeature(f)).filter(f -> !f.getRange().isPrimitive()).collect(Collectors.toList());
    // ... there are exactly two non-primitive features
    if (nonPrimitiveFeatures.size() != 2) {
        return Optional.empty();
    }
    Feature ref1 = nonPrimitiveFeatures.get(0);
    Feature ref2 = nonPrimitiveFeatures.get(1);
    // Relations must use the names "Governor" and "Dependent" for its references because
    // these names are hardcoded throughout WebAnno.
    List<String> validNames = asList(FEAT_REL_SOURCE, FEAT_REL_TARGET);
    if (!validNames.contains(ref1.getShortName()) || !validNames.contains(ref2.getShortName())) {
        return Optional.empty();
    }
    // ... both have the same range
    if (!ref1.getRange().getName().equals(ref2.getRange().getName())) {
        return Optional.empty();
    }
    // Annotation should be fine.
    if (!aTS.subsumes(aTS.getType(CAS.TYPE_NAME_ANNOTATION), ref1.getRange())) {
        return Optional.empty();
    }
    RelationDetails details = new RelationDetails();
    details.attachLayer = ref1.getRange().getName();
    details.sourceFeature = WebAnnoConst.FEAT_REL_SOURCE;
    details.targetFeature = WebAnnoConst.FEAT_REL_TARGET;
    // Hm, ok, so this looks like a relation layer.
    return Optional.of(details);
}

Example 10 with Range

use of org.apache.commons.lang3.Range in project photon-model by vmware.

the class IPAddressAllocationTaskService method createNewIpAddressResource.

/**
 * Creates new IP address resource with the specified IP address and moves the task state to completed,
 * once it is done. Then it creates IP Address resource, it first creates it with AVAILABLE state. It then
 * changes the state to ALLOCATED. This is done in two steps, due to concurrency issues. When multiple allocation
 * requests are invoked at the same time, they end up creating single IP Address resource. Only one of them
 * succeeds in their PATCH and the other one will retry the allocation operation.
 *
 * @param ipAddress               IP address to use for the new IP address resource.
 * @param subnetRangeResourceLink Subnet range resource link to use for the new IP address resource.
 * @param connectedResourceLink   Link to the resource this IP is assigned to.
 */
private DeferredResult<IPAddressState> createNewIpAddressResource(String ipAddress, String subnetRangeResourceLink, String connectedResourceLink, IPAddressAllocationContext context) {
    IPAddressState ipAddressState = new IPAddressState();
    ipAddressState.ipAddressStatus = IPAddressState.IPAddressStatus.AVAILABLE;
    ipAddressState.ipAddress = ipAddress;
    ipAddressState.subnetRangeLink = subnetRangeResourceLink;
    ipAddressState.documentSelfLink = generateIPAddressDocumentSelfLink(subnetRangeResourceLink, ipAddress);
    logInfo("Creating IPAddressState with IP %s, subnet %s, for connected resource " + "%s", ipAddress, subnetRangeResourceLink, connectedResourceLink);
    return sendWithDeferredResult(Operation.createPost(this, IPAddressService.FACTORY_LINK).setBody(ipAddressState)).thenApply((out) -> {
        IPAddressState availableIPAddress = out.getBody(IPAddressState.class);
        availableIPAddress.ipAddressStatus = IPAddressState.IPAddressStatus.ALLOCATED;
        availableIPAddress.connectedResourceLink = connectedResourceLink;
        return availableIPAddress;
    }).thenCompose((availableIPAddress) -> (updateExistingIpAddressResource(availableIPAddress, context)));
}