Package picard.util

Examples of picard.util.BasicInputParser

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    /**
     * Prepare to iterate.
     */
    private void initializeParser() {
        final List<File> fileSubset = files.getFilesStartingAt(currentTile);
        parser = new BasicInputParser(treatGroupedDelimitersAsOne, fileSubset.toArray(new File[fileSubset.size()]));
    }
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    private static final int Y_OR_N_COLUMN = 1;
    private static final int BARCODE_COLUMN = 2;
    private final BasicInputParser textIterator;

    public BarcodeFileReader(final File barcodeFile) {
        this.textIterator = new BasicInputParser(false, barcodeFile);
    }
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    private final BasicInputParser parser;

    public PosFileReader(final File posFile) {
        super(posFile);
        this.parser  = new BasicInputParser(true, posFile);
    }
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        // Check the barcode files themselves
        final File[] barcodeFiles = IOUtil.getFilesMatchingRegexp(basecallsDir, "s_" + lane + "_\\d{4}_barcode.txt");
        Arrays.sort(barcodeFiles);

        final BasicInputParser barcodeParser = new BasicInputParser(true, barcodeFiles);

        // Exact match
        String[] illuminaFields = barcodeParser.next();
        Assert.assertEquals(illuminaFields[1], "Y");
        Assert.assertEquals(illuminaFields[2], "CAACTCTC");

        // Inexact match
        illuminaFields = barcodeParser.next();
        Assert.assertEquals(illuminaFields[1], "Y");
        Assert.assertEquals(illuminaFields[2], "ACAGGTAT");

        // Too many mismatches
        illuminaFields = barcodeParser.next();
        Assert.assertEquals(illuminaFields[1], "N");

        barcodeParser.close();

        // Tack on test of barcode-informed Illumina Basecall parsing
        final ReadStructure rs = new ReadStructure("25T8B25T");
        final IlluminaDataProviderFactory factory = new IlluminaDataProviderFactory(basecallsDir, lane, rs,
                new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY),
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Related Classes of picard.util.BasicInputParser

  • htsjdk.samtools.util.BufferedLineReader
  • picard.illumina.ExtractIlluminaBarcodesTest
  • picard.illumina.parser.IlluminaTextIterator
  • picard.illumina.parser.readers.BarcodeFileReader
  • picard.illumina.parser.readers.PosFileReader
  • java.io.InputStream
  • picard.PicardException
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