entityAttributeNameSet.add(attribute.getName()); if (attribute.getName().equals("GATKDepthOfCoverage.totalCoverage")) { attribute.setValue(split[1]); break; if (attribute.getName().equals("GATKDepthOfCoverage.mean")) { attribute.setValue(split[1]); break; if ("SAMToolsFlagstat.totalPassedReads".equals(attribute.getName())) { totalPassedReads = Long.valueOf(attribute.getValue()); break; if (attribute.getName().equals("sample_interval_summary.totalCoverageCount")) { attribute.setValue(totalCoverageCount + ""); break; if (synchSet.contains("numberOnTarget")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("numberOnTarget") && totalPassedReads != null) { attribute.setValue((double) totalCoverageCount / (totalPassedReads * 100) + ""); break;
entityAttributeNameSet.add(attribute.getName()); if (synchSet.contains("SAMToolsFlagstat.totalPassedReads")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("SAMToolsFlagstat.totalPassedReads")) { attribute.setValue(value); break; if (synchSet.contains("SAMToolsFlagstat.aligned")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("SAMToolsFlagstat.aligned")) { attribute.setValue(value); break; if (synchSet.contains("SAMToolsFlagstat.paired")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("SAMToolsFlagstat.paired")) { attribute.setValue(value); break;
entityAttributeNameSet.add(attribute.getName()); if (synchSet.contains("yield")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("yield")) { attribute.setValue(value); break; if (synchSet.contains("passedFiltering")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("passedFiltering")) { attribute.setValue(value); break; if (synchSet.contains("numberOfReads")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("numberOfReads")) { attribute.setValue(value); break; if (synchSet.contains("rawClustersPerLane")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("rawClustersPerLane")) { attribute.setValue(value); break; if (synchSet.contains("perfectIndexReads")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("perfectIndexReads")) {
entityAttributeNameSet.add(attribute.getName()); if (synchSet.contains("PicardMarkDuplicates.readPairDuplicates")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("PicardMarkDuplicates.readPairDuplicates")) { attribute.setValue(readPairDuplicates); break; if (synchSet.contains("PicardMarkDuplicates.percentDuplication")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("PicardMarkDuplicates.percentDuplication")) { attribute.setValue(percentDuplication); break;
while (attributeIter.hasNext()) { EntityAttribute attribute = attributeIter.next(); String name = attribute.getName(); String value = attribute.getValue(); if ("subjectName".equals(name)) {
while (attributeIter.hasNext()) { EntityAttribute attribute = attributeIter.next(); if ("GATKDepthOfCoverage.prefix".equals(attribute.getName())) { prefix = attribute.getValue(); entityAttributeNameSet.add(attribute.getName()); if (synchSet.contains(totalCoverageKey)) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals(totalCoverageKey)) { attribute.setValue(split[1]); break; if (synchSet.contains(meanCoverageKey)) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals(meanCoverageKey)) { attribute.setValue(split[1]); break; if ("SAMToolsFlagstat.totalPassedReads".equals(attribute.getName())) { totalPassedReads = Long.valueOf(attribute.getValue()); break; if (attribute.getName().equals(totalCoverageCountKey)) { attribute.setValue(totalCoverageCount + ""); break; if (synchSet.contains(numberOnTargetKey)) { for (EntityAttribute attribute : attributeSet) {
if (entityAttribute.getName().equals("identity_confirmed")) { entityAttribute.setValue(null); break;
while (attributeIter.hasNext()) { EntityAttribute attribute = attributeIter.next(); if ("GATKDepthOfCoverage.intervalList".equals(attribute.getName())) { intervalList = attribute.getValue(); if ("GATKDepthOfCoverage.prefix".equals(attribute.getName())) { prefix = attribute.getValue(); if ("GATKDepthOfCoverage.summaryCoverageThreshold".equals(attribute.getName())) { summaryCoverageThreshold = attribute.getValue();
while (attributeIter.hasNext()) { EntityAttribute attribute = attributeIter.next(); if ("isIncidental".equals(attribute.getName())) { isIncidental = Boolean.TRUE; if ("GATKDepthOfCoverage.interval_list.version".equals(attribute.getName())) { version = attribute.getValue(); if ("SAMToolsView.dx.id".equals(attribute.getName())) { dx = attribute.getValue();
while (attributeIter.hasNext()) { EntityAttribute attribute = attributeIter.next(); if ("GATKVariantRecalibrator.percentBadVariants".equals(attribute.getName())) { percentBadVariants = attribute.getValue();