private static String moiAbbreviation(ModeOfInheritance modeOfInheritance) { String moiAbbreviation = modeOfInheritance.getAbbreviation(); return moiAbbreviation == null ? "" : "_" + moiAbbreviation; }
@Override public String writeString(ModeOfInheritance modeOfInheritance, Analysis analysis, AnalysisResults analysisResults, OutputSettings settings) { //Add prettyPrintJson option to outputSettings? ObjectWriter objectWriter = new ObjectMapper().writerWithDefaultPrettyPrinter(); try (Writer stringWriter = new StringWriter()) { writeData(modeOfInheritance, analysisResults, settings.outputContributingVariantsOnly(), objectWriter, stringWriter); stringWriter.flush(); logger.info("{} {} results written to string", OUTPUT_FORMAT, (modeOfInheritance.getAbbreviation() == null) ? "ALL" : modeOfInheritance .getAbbreviation()); return stringWriter.toString(); } catch (IOException ex) { logger.error("Unable to write results to json.", ex); } return ""; }
@Override public void writeFile(ModeOfInheritance modeOfInheritance, Analysis analysis, AnalysisResults analysisResults, OutputSettings settings) { String outFileName = ResultsWriterUtils.makeOutputFilename(analysis.getVcfPath(), settings.getOutputPrefix(), OUTPUT_FORMAT, modeOfInheritance); Path outFile = Paths.get(outFileName); ObjectWriter objectWriter = new ObjectMapper().writer(); try (Writer bufferedWriter = Files.newBufferedWriter(outFile, StandardCharsets.UTF_8)) { writeData(modeOfInheritance, analysisResults, settings.outputContributingVariantsOnly(), objectWriter, bufferedWriter); } catch (IOException ex) { logger.error("Unable to write results to file {}", outFileName, ex); } logger.info("{} {} results written to file {}", OUTPUT_FORMAT, (modeOfInheritance.getAbbreviation() == null) ? "ALL" : modeOfInheritance .getAbbreviation(), outFileName); }
@Override public void writeFile(ModeOfInheritance modeOfInheritance, Analysis analysis, AnalysisResults analysisResults, OutputSettings settings) { String outFileName = ResultsWriterUtils.makeOutputFilename(analysis.getVcfPath(), settings.getOutputPrefix(), OUTPUT_FORMAT, modeOfInheritance); Path outFile = Paths.get(outFileName); try (CSVPrinter printer = new CSVPrinter(Files.newBufferedWriter(outFile, StandardCharsets.UTF_8), format)) { writeData(modeOfInheritance, analysisResults, printer); } catch (IOException ex) { logger.error("Unable to write results to file {}", outFileName, ex); } logger.info("{} {} results written to file {}", OUTPUT_FORMAT, modeOfInheritance.getAbbreviation(), outFileName); }
@Override public void writeFile(ModeOfInheritance modeOfInheritance, Analysis analysis, AnalysisResults analysisResults, OutputSettings settings) { String outFileName = ResultsWriterUtils.makeOutputFilename(analysis.getVcfPath(), settings.getOutputPrefix(), OUTPUT_FORMAT, modeOfInheritance); Path outFile = Paths.get(outFileName); try (CSVPrinter printer = new CSVPrinter(Files.newBufferedWriter(outFile, StandardCharsets.UTF_8), format)) { writeData(modeOfInheritance, analysis, analysisResults, settings.outputContributingVariantsOnly(), printer); } catch (IOException ex) { logger.error("Unable to write results to file {}", outFileName, ex); } logger.info("{} {} results written to file {}", OUTPUT_FORMAT, modeOfInheritance.getAbbreviation(), outFileName); }
@Override public void writeFile(ModeOfInheritance modeOfInheritance, Analysis analysis, AnalysisResults analysisResults, OutputSettings settings) { // create a VariantContextWriter writing to the output file path String outFileName = ResultsWriterUtils.makeOutputFilename(analysis.getVcfPath(), settings.getOutputPrefix(), OUTPUT_FORMAT, modeOfInheritance); Path outFile = Paths.get(outFileName); VCFHeader vcfHeader = getVcfHeader(analysis); try (VariantContextWriter writer = VariantContextWriterConstructionHelper.openVariantContextWriter( vcfHeader, outFile.toString(), getAdditionalHeaderLines(), false)) { writeData(modeOfInheritance, analysisResults, settings.outputContributingVariantsOnly(), writer); } logger.info("{} {} results written to file {}.", OUTPUT_FORMAT, modeOfInheritance.getAbbreviation(), outFileName); }
modes.addAll(var.getCompatibleModes().stream().map(m -> m.toModeOfInheritance().getAbbreviation()) .filter(m -> m != null).collect(Collectors.toList())); ArrayList<String> arSubModes = new ArrayList<>();