/** * Handle writing the {@link BasicStats} to the database. * * @param stats the {@link BasicStats} computed by fastqc. * @param analysis the {@link AnalysisFastQCBuilder} to update. */ private void handleBasicStats(BasicStats stats, AnalysisFastQCBuilder analysis) { analysis.fileType(stats.getFileType()); analysis.encoding(PhredEncoding.getFastQEncodingOffset(stats.getLowestChar()).name()); analysis.minLength(stats.getMinLength()); analysis.maxLength(stats.getMaxLength()); analysis.totalSequences(stats.getActualCount()); analysis.filteredSequences(stats.getFilteredCount()); analysis.gcContent(stats.getGCContent()); analysis.totalBases( stats.getACount() + stats.getGCount() + stats.getCCount() + stats.getTCount() + stats.getNCount()); }