Examples with PerSequenceQualityScores uk.ac.babraham.FastQC.Modules.PerSequenceQualityScores used on opensource projects

Example 1 with PerSequenceQualityScores

use of uk.ac.babraham.FastQC.Modules.PerSequenceQualityScores in project irida by phac-nml.

the class FastqcFileProcessor method processSingleFile.

/**
 * Process a single {@link SequenceFile}
 *
 * @param sequenceFile
 *            file to process
 * @throws FileProcessorException
 *             if an error occurs while processing
 */
private void processSingleFile(SequenceFile sequenceFile) throws FileProcessorException {
    Path fileToProcess = sequenceFile.getFile();
    AnalysisFastQC.AnalysisFastQCBuilder analysis = AnalysisFastQC.builder().executionManagerAnalysisId(EXECUTION_MANAGER_ANALYSIS_ID).description(messageSource.getMessage("fastqc.file.processor.analysis.description", null, LocaleContextHolder.getLocale()));
    try {
        uk.ac.babraham.FastQC.Sequence.SequenceFile fastQCSequenceFile = SequenceFactory.getSequenceFile(fileToProcess.toFile());
        BasicStats basicStats = new BasicStats();
        PerBaseQualityScores pbqs = new PerBaseQualityScores();
        PerSequenceQualityScores psqs = new PerSequenceQualityScores();
        OverRepresentedSeqs overRep = new OverRepresentedSeqs();
        QCModule[] moduleList = new QCModule[] { basicStats, pbqs, psqs, overRep };
        logger.debug("Launching FastQC analysis modules on all sequences.");
        while (fastQCSequenceFile.hasNext()) {
            Sequence sequence = fastQCSequenceFile.next();
            for (QCModule module : moduleList) {
                module.processSequence(sequence);
            }
        }
        logger.debug("Finished FastQC analysis modules.");
        handleBasicStats(basicStats, analysis);
        handlePerBaseQualityScores(pbqs, analysis);
        handlePerSequenceQualityScores(psqs, analysis);
        handleDuplicationLevel(overRep.duplicationLevelModule(), analysis);
        Set<OverrepresentedSequence> overrepresentedSequences = handleOverRepresentedSequences(overRep);
        logger.trace("Saving FastQC analysis.");
        analysis.overrepresentedSequences(overrepresentedSequences);
        sequenceFile.setFastQCAnalysis(analysis.build());
        sequenceFileRepository.saveMetadata(sequenceFile);
    } catch (Exception e) {
        logger.error("FastQC failed to process the sequence file. Stack trace follows.", e);
        throw new FileProcessorException("FastQC failed to parse the sequence file.", e);
    }
}