Examples of BclData

picard.illumina.parser.BclData
A class that implements the IlluminaData interfaces provided by this parser One BclData object is returned to IlluminaDataProvider per cluster and each first level array in bases and qualities represents a single read in that cluster

Examples of picard.illumina.parser.BclData

    public BclData next() {
        if (queue == null) {
            advance();
        }


        final BclData data = queue;
        queue = null;
        return data;
    }

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Examples of picard.illumina.parser.BclData

        throw new UnsupportedOperationException();
    }


    void advance() {
        int totalCycleCount = 0;
        final BclData data = new BclData(outputLengths);
        for (int read = 0; read < outputLengths.length; read++) {
            for (int cycle = 0; cycle < outputLengths[read]; ++cycle) {
                try {
                    final int readByte = this.streams[totalCycleCount].read();
                    if (readByte == -1) {

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Examples of picard.illumina.parser.BclData


        Assert.assertEquals(reader.numClustersPerCycle[0], expectedBases.length);


        int readNum = 0;
        while (readNum < reader.numClustersPerCycle[0]) {
            final BclData bv = reader.next();
            Assert.assertEquals(bv.bases[0][0], expectedBases[readNum], " On num cluster: " + readNum);
            Assert.assertEquals(bv.qualities[0][0], quals[readNum], " On num cluster: " + readNum);
            ++readNum;
        }
        bclQualityEvaluationStrategy.assertMinimumQualities();

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