if (!laneClusterDensityTotalMap.containsKey(sample.getLaneIndex())) { laneClusterDensityTotalMap.put(sample.getLaneIndex(), new ArrayList<Double>()); List<Double> laneClusterDensityTotalList = laneClusterDensityTotalMap.get(sample.getLaneIndex()); long clusterDensityTotal = 0; for (Double clusterDensity : laneClusterDensityTotalList) {
sequencerRun.getName(), htsfSample.getLaneIndex()); logger.debug("readPairList.size(): {}", readPairList.size()); String laneStr = String.format("L%03d", htsfSample.getLaneIndex());
htsfSample.getLaneIndex());
sample.getLaneIndex())); File baseCallStatsDir = new File(unalignedDir, String.format("Basecall_Stats_%s", flowcell)); File statsFile = new File(baseCallStatsDir, "Demultiplex_Stats.htm"); && sample.getLaneIndex().toString().equals(laneElement.text()) && sample.getBarcode().equals(indexElement.text())) {
Integer laneIndex = htsfSample.getLaneIndex(); logger.debug("laneIndex = {}", laneIndex); Set<FileData> fileDataSet = htsfSample.getFileDatas();
.toLowerCase()); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, String.format("%s-%s_L%03d", sequencerRun.getName(), htsfSample.getBarcode(), htsfSample.getLaneIndex())); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, htsfSample.getBarcode()); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, String.format("L%03d_%s", htsfSample.getLaneIndex(), htsfSample.getBarcode())); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, String.format("L%03d_%s", htsfSample.getLaneIndex(), htsfSample.getBarcode())); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPCENTERNAME, "UNC");
String newSampleName = String.format("L%03d_%s", htsfSample.getLaneIndex(), htsfSample.getBarcode()); logger.info("newSampleName: {}", newSampleName); sequencerRun.getName(), htsfSample.getLaneIndex()); String laneStr = String.format("L%03d", htsfSample.getLaneIndex());
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName()); Integer laneIndex = htsfSample.getLaneIndex(); logger.debug("laneIndex = {}", laneIndex); List<File> readPairList = PipelineUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex()); logger.info("fileList = {}", readPairList.size());
Integer laneIndex = htsfSample.getLaneIndex(); logger.debug("laneIndex = {}", laneIndex); Set<FileData> fileDataSet = htsfSample.getFileDatas();
Integer laneIndex = htsfSample.getLaneIndex(); logger.debug("laneIndex = {}", laneIndex); Set<FileData> fileDataSet = htsfSample.getFileDatas();
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName()); Integer laneIndex = htsfSample.getLaneIndex(); logger.debug("laneIndex = {}", laneIndex); List<File> readPairList = PipelineUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex()); logger.info("fileList = {}", readPairList.size());
htsfSample.getLaneIndex()); logger.info("fileList = {}", readPairList.size());
htsfSample.getLaneIndex()); logger.debug("fileList = {}", readPairList.size());
htsfSample.getLaneIndex()); logger.debug("fileList = {}", readPairList.size());
htsfSample.getLaneIndex()); logger.debug("fileList = {}", readPairList.size());
Integer laneIndex = htsfSample.getLaneIndex(); logger.debug("laneIndex = {}", laneIndex);
getName().replace("VariantCalling", ""), getVersion()); Integer laneIndex = htsfSample.getLaneIndex(); logger.debug("laneIndex = {}", laneIndex); Set<FileData> fileDataSet = htsfSample.getFileDatas();
getName().replace("VariantCalling", ""), getVersion()); Integer laneIndex = htsfSample.getLaneIndex(); logger.debug("laneIndex = {}", laneIndex); Set<FileData> fileDataSet = htsfSample.getFileDatas();