getName().replace("Clean", ""), getVersion()); logger.debug("htsfSample = {}", htsfSample.toString()); List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex());
logger.info("htsfSample: {}", htsfSample.toString());
logger.info("htsfSample: {}", htsfSample.toString()); continue;
mapseqDAOBean.getHTSFSampleDAO().save(sample); System.out.println(String.format("Successfully saved sample: %s", sample.getId())); logger.info(sample.toString());
logger.warn("vcf file to process was not found: {}", htsfSample.toString()); return;
System.out.println("FINISHED PROCESSING: " + htsfSample.toString());
logger.info("htsfSample: {}", htsfSample.toString());
logger.debug("Found HTSFSample: {}", htsfSample.toString()); return htsfSample;
logger.debug("Found HTSFSample: {}", htsfSample.toString()); return htsfSample;
logger.warn("vcf file to process was not found: {}", htsfSample.toString()); throw new WorkflowException("vcf file to process was not found");
logger.debug("htsfSample = {}", htsfSample.toString());
logger.debug("htsfSample = {}", htsfSample.toString());
File outputDirectory = createOutputDirectory(sequencerRun.getName(), htsfSample, getName(), getVersion()); logger.info("htsfSample: {}", htsfSample.toString()); List<File> readPairList = WorkflowUtil.getReadPairList(htsfSample.getFileDatas(), sequencerRun.getName(), htsfSample.getLaneIndex());
getName().replace("VariantCalling", ""), getVersion()); logger.info("htsfSample: {}", htsfSample.toString()); Set<FileData> fileDataSet = htsfSample.getFileDatas();