Package htsjdk.samtools.util

Examples of htsjdk.samtools.util.QualityEncodingDetector


        System.exit(new FastqToSam().instanceMain(argv));
    }

    /* Simply invokes the right method for unpaired or paired data. */
    protected int doWork() {
            final QualityEncodingDetector detector = new QualityEncodingDetector();
            final FastqReader reader = new FastqReader(FASTQ,ALLOW_AND_IGNORE_EMPTY_LINES);
            if (FASTQ2 == null) {
                detector.add(QualityEncodingDetector.DEFAULT_MAX_RECORDS_TO_ITERATE, reader);
            } else {
                final FastqReader reader2 = new FastqReader(FASTQ2,ALLOW_AND_IGNORE_EMPTY_LINES);
                detector.add(QualityEncodingDetector.DEFAULT_MAX_RECORDS_TO_ITERATE, reader, reader2);
                reader2.close();
            }
            reader.close();
           
            QUALITY_FORMAT = detector.generateBestGuess(QualityEncodingDetector.FileContext.FASTQ, QUALITY_FORMAT);
            if (detector.isDeterminationAmbiguous())
                LOG.warn("Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities.");
            LOG.info(String.format("Auto-detected quality format as: %s.", QUALITY_FORMAT));

        final int readCount = (FASTQ2 == null) ?  doUnpaired() : doPaired();
        LOG.info("Processed " + readCount + " fastq reads");
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