Examples of picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat

Package picard.illumina.parser.IlluminaFileUtil

Examples of picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat

picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat

        final SortedSet<IlluminaDataType> toSupport = new TreeSet<IlluminaDataType>(requestedDataTypes);
        final Map<SupportedIlluminaFormat, Set<IlluminaDataType>> fileTypeToDataTypes = new HashMap<SupportedIlluminaFormat, Set<IlluminaDataType>>();
        final Map<IlluminaDataType, SupportedIlluminaFormat> dataTypeToFormat = new HashMap<IlluminaDataType, SupportedIlluminaFormat>();


        for (final IlluminaDataType ts : toSupport) {
            final SupportedIlluminaFormat preferredFormat = findPreferredAvailableFormat(ts, fileUtil);
            if (preferredFormat != null) {
                dataTypeToFormat.put(ts, preferredFormat);
            }
        }


        for (final IlluminaDataType dt : toSupport) {
            final SupportedIlluminaFormat format = dataTypeToFormat.get(dt);


            if (format != null) {
                if (fileTypeToDataTypes.containsKey(format)) {
                    fileTypeToDataTypes.get(format).add(dt);
                } else {

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    }


    private static SupportedIlluminaFormat findPreferredFormat(final IlluminaDataType dt, final IlluminaFileUtil fileUtil,
                                                               final boolean checkAvailable) {
        final List<SupportedIlluminaFormat> preferredFormats = DATA_TYPE_TO_PREFERRED_FORMATS.get(dt);
        SupportedIlluminaFormat format = null;
        for (int i = 0; i < preferredFormats.size() && format == null; i++) {
            if (checkAvailable && fileUtil.getUtil(preferredFormats.get(i)).filesAvailable()) {
                format = preferredFormats.get(i);
            } else if (!checkAvailable) {
                format = preferredFormats.get(i);

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        };
    }


    @Test(expectedExceptions = PicardException.class, dataProvider = "missingCycleDataRanges")
    public void perTilePerCycleFileUtilsMissingCycleTest(final List<Range> cycleRangesToMake) {
        final SupportedIlluminaFormat format = SupportedIlluminaFormat.Bcl;


        for (final Range range : cycleRangesToMake) {
            makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, cycleRange(range), null);
        }

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Related Classes of picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat

picard.illumina.parser.IlluminaDataProviderFactory

picard.illumina.parser.IlluminaFileUtilTest

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