Java Code Examples for org.broadinstitute.barclay.utils.Utils#nonNull()
The following examples show how to use
org.broadinstitute.barclay.utils.Utils#nonNull() .
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Example 1
Source File: PropertyUtils.java From picard with MIT License | 6 votes |
/** * Attempt to load a Properties object from an on-disk properties file. * @param propertyFilePath name of the properties file to load. Must have a .properties extension * @param clazz class used to obtain a class loader to use to locate the properties file * @return null if the files doesn't exist or isn't readable, otherwise a Properties object */ public static Properties loadPropertiesFile(final String propertyFilePath, final Class<?> clazz) { Utils.nonNull(propertyFilePath); try (final InputStream inputStream = clazz.getClassLoader().getResourceAsStream(propertyFilePath)) { if (inputStream != null) { final Properties properties = new Properties(); properties.load(inputStream); return properties; } else { return null; } } catch (IOException ex) { throw new RuntimeException(String.format("IOException loading properties file %s", propertyFilePath), ex); } }
Example 2
Source File: SimpleAnnotatedIntervalWriter.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
/** * @param annotatedIntervalHeader Header to write. Recommended to create the header using * {@link AnnotatedIntervalCodec#createHeaderForWriter(Path, List, SAMFileHeader)} or one of its overloaded * versions. Never {@code null} */ @Override public void writeHeader(final AnnotatedIntervalHeader annotatedIntervalHeader) { Utils.nonNull(annotatedIntervalHeader); if (!hasHeaderBeenWritten) { final String contigColumnName = annotatedIntervalHeader.getContigColumnName(); final String startColumnName = annotatedIntervalHeader.getStartColumnName(); final String endColumnName = annotatedIntervalHeader.getEndColumnName(); initializeForWriting(contigColumnName, startColumnName, endColumnName, annotatedIntervalHeader.getAnnotations()); try { final SAMFileHeader samFileHeader = annotatedIntervalHeader.getSamFileHeader(); if (samFileHeader != null) { fileWriter.write(samFileHeader.getSAMString()); } writer.writeHeaderIfApplies(); hasHeaderBeenWritten = true; } catch (final IOException e) { throw new UserException.CouldNotCreateOutputFile("Could not write to file.", e); } } else { logger.warn("Attempted to write header more than once. Ignoring this request."); } }
Example 3
Source File: CalledLegacySegmentCollection.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
@Override public void write(final File outputFile) { Utils.nonNull(outputFile); try (final RecordCollectionWriter writer = new RecordCollectionWriter(new FileWriter(outputFile))) { writer.writeAllRecords(getRecords()); } catch (final IOException e) { throw new UserException.CouldNotCreateOutputFile(outputFile, e); } }
Example 4
Source File: VcfFuncotationMetadata.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
/** * @param vcfInfoHeaderLines Never {@code null} * @return Metadata corresponding to VCF info fields. Never {@code null} */ public static VcfFuncotationMetadata create(final List<VCFInfoHeaderLine> vcfInfoHeaderLines) { Utils.nonNull(vcfInfoHeaderLines); return new VcfFuncotationMetadata( vcfInfoHeaderLines.stream().collect(Collectors.toMap(v -> v.getID(), Function.identity(), (x1,x2) -> x2, LinkedHashMap::new )) ); }
Example 5
Source File: DataSourceFuncotationFactory.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
/** * Creates a {@link List} of {@link Funcotation} for the given {@code variant}, {@code referenceContext}, {@code featureContext}, and {@code gencodeFuncotations}. * For some Data Sources knowledge of Gene Name or Transcript ID is required for annotation. * Accounts for override values passed into the constructor as well. * @param variant {@link VariantContext} to annotate. Never {@code null}. * @param referenceContext {@link ReferenceContext} corresponding to the given {@code variant}. Never {@code null}. * @param featureContext {@link FeatureContext} corresponding to the variant. Never {@code null}. * @param gencodeFuncotations {@link List} of {@link GencodeFuncotation} that have already been created for the given {@code variant}/{@code referenceContext}/{@code featureContext}. * {@code null} is acceptable if there are no corresponding gencode funcotations. * @return {@link List} of {@link Funcotation} given the {@code variant}, {@code referenceContext}, and {@code featureContext}. This should never be empty. */ public List<Funcotation> createFuncotations(final VariantContext variant, final ReferenceContext referenceContext, final FeatureContext featureContext, final List<GencodeFuncotation> gencodeFuncotations) { Utils.nonNull(variant); Utils.nonNull(referenceContext); Utils.nonNull(featureContext); final List<Funcotation> outputFuncotations; // Query this funcotation factory to get the list of overlapping features. // NOTE: This will only get features that are LOCATABLE! // This corresponds to requiresFeatures() returning `True`. final List<Feature> featureList = getFeaturesFromFeatureContext(featureContext); // If our featureList is compatible with this DataSourceFuncotationFactory, then we make our funcotations: if ( isFeatureListCompatible(featureList) ) { outputFuncotations = determineFuncotations(variant, referenceContext, featureList, gencodeFuncotations); // Set our overrides: setOverrideValuesInFuncotations(outputFuncotations); } else { return createDefaultFuncotationsOnVariant(variant, referenceContext); } if ((outputFuncotations == null) || (outputFuncotations.size() == 0)) { return createDefaultFuncotationsOnVariant(variant, referenceContext); } else { return outputFuncotations; } }
Example 6
Source File: XHMMEmissionProbabilityCalculator.java From gatk-protected with BSD 3-Clause "New" or "Revised" License | 4 votes |
public double generateRandomZScoreData(final double copyRatio) { Utils.nonNull(rng, "Random z-score sampling is called by the random number generator is null. This" + " instance of the class can not produce random samples."); return getEmissionMean(copyRatio) + rng.nextGaussian() * emissionStandardDeviation; }
Example 7
Source File: IntegerCopyNumberReferenceStateFactory.java From gatk-protected with BSD 3-Clause "New" or "Revised" License | 4 votes |
public IntegerCopyNumberReferenceStateFactory(@Nonnull final GermlinePloidyAnnotatedTargetCollection germlinePloidyAnnotatedTargetCollection) { this.germlinePloidyAnnotatedTargetCollection = Utils.nonNull(germlinePloidyAnnotatedTargetCollection); }