if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
&& sample.getBarcode().equals(indexElement.text())) {
.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");
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) { continue;
if ("Undetermined".equals(htsfSample.getBarcode())) {continue;}