Examples of BclReader

picard.illumina.parser.readers.BclReader
BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters. The file is structured as followed: Bytes 1-4 : unsigned int numClusters Bytes 5-numClusters + 5 : 1 byte base/quality score
The base/quality scores are organized as follows (with one exception, SEE BELOW): The right 2 most bits (these are the LEAST significant bits) indicate the base, where A=00(0x00), C=01(0x01), G=10(0x02), and T=11(0x03)
The remaining bytes compose the quality score which is an unsigned int.
EXCEPTION: If a byte is entirely 0 (e.g. byteRead == 0) then it is a no call, the base becomes '.' and the Quality becomes 2, the default illumina masking value
(E.g. if we get a value in binary of 10001011 it gets transformed as follows:
Value read: 10001011(0x8B)
Quality Base
100010 11 00100010 0x03 0x22 T 34 T
So the output base/quality will be a (T/34)

Examples of picard.illumina.parser.readers.BclReader


    private class BclDataCycleFileParser implements CycleFilesParser<BclData> {
        final CloseableIterator<BclData> reader;


        public BclDataCycleFileParser(final List<File> files) {
            reader = new BclReader(files, outputMapping.getOutputReadLengths(),
                    bclQualityEvaluationStrategy, false);
        }

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Examples of picard.illumina.parser.readers.BclReader

        }
    }


    private CountLimitedIterator makeReader(final List<File> files) {
        if(tileIndex != null) {
            final BclReader bclReader = BclReader.makeSeekable(files, bclQualityEvaluationStrategy, outputMapping.getOutputReadLengths());
            final int numClustersInTile = bclReader.seek(files, tileIndex, currentTile);
            return new CountLimitedIterator(bclReader, numClustersInTile);
        }
        else{
            return null;
        }

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Examples of picard.illumina.parser.readers.BclReader

        final File fakeFile = File.createTempFile("BclFileFakerTest", ".bcl");
        fakeFile.deleteOnExit();


        new BclFileFaker().fakeFile(fakeFile, 100000);
        // .make() has a number of checks for the file
        final BclReader bclReader = new BclReader(
            fakeFile,
            new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY), false);
        Assert.assertEquals(100000, BclReader.getNumberOfClusters(fakeFile));
        Assert.assertEquals(BclReader.getNumberOfClusters(fakeFile), fakeFile.length() - 4);
    }

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Examples of picard.illumina.parser.readers.BclReader

    public void testGZFileIsActuallyGZipped() throws Exception {
        final File fakeFile = File.createTempFile("BclFileFakerTest", ".bcl.gz");
        fakeFile.deleteOnExit();


        new BclFileFaker().fakeFile(fakeFile, 100000);
        new BclReader(
                fakeFile,
                new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY), false);
    }

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