entityAttributeNameSet.add(attribute.getName()); if (synchSet.contains("SAMToolsFlagstat.totalPassedReads")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("SAMToolsFlagstat.totalPassedReads")) { attribute.setValue(value); break; attributeSet.add(new EntityAttribute("SAMToolsFlagstat.totalPassedReads", value)); if (synchSet.contains("SAMToolsFlagstat.aligned")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("SAMToolsFlagstat.aligned")) { attribute.setValue(value); break; attributeSet.add(new EntityAttribute("SAMToolsFlagstat.aligned", value)); if (synchSet.contains("SAMToolsFlagstat.paired")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("SAMToolsFlagstat.paired")) { attribute.setValue(value); break; attributeSet.add(new EntityAttribute("SAMToolsFlagstat.paired", value));
attributeNameSet.add(attribute.getName()); EntityAttribute attribute = new EntityAttribute(); attribute.setName(attributeName); attribute.setValue(attributeValue); attributeSet.add(attribute); } else { for (EntityAttribute attribute : attributeSet) { if (attributeName.equals(attribute.getName())) { attribute.setValue(attributeValue);
entityAttributeNameSet.add(attribute.getName()); if (attribute.getName().equals("GATKDepthOfCoverage.totalCoverage")) { attribute.setValue(split[1]); break; .add(new EntityAttribute("GATKDepthOfCoverage.totalCoverage", split[1])); if (attribute.getName().equals("GATKDepthOfCoverage.mean")) { attribute.setValue(split[1]); break; attributeSet.add(new EntityAttribute("GATKDepthOfCoverage.mean", split[2])); if ("SAMToolsFlagstat.totalPassedReads".equals(attribute.getName())) { totalPassedReads = Long.valueOf(attribute.getValue()); break; if (attribute.getName().equals("sample_interval_summary.totalCoverageCount")) { attribute.setValue(totalCoverageCount + ""); break; attributeSet.add(new EntityAttribute("sample_interval_summary.totalCoverageCount", totalCoverageCount + "")); if (synchSet.contains("numberOnTarget")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("numberOnTarget") && totalPassedReads != null) { attribute.setValue((double) totalCoverageCount / (totalPassedReads * 100) + "");
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; attributeSet.add(new EntityAttribute(totalCoverageKey, split[1])); if (synchSet.contains(meanCoverageKey)) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals(meanCoverageKey)) { attribute.setValue(split[1]); break; attributeSet.add(new EntityAttribute(meanCoverageKey, split[2])); if ("SAMToolsFlagstat.totalPassedReads".equals(attribute.getName())) { totalPassedReads = Long.valueOf(attribute.getValue()); break; if (attribute.getName().equals(totalCoverageCountKey)) { attribute.setValue(totalCoverageCount + "");
entityAttributeNameSet.add(attribute.getName()); if (synchSet.contains("yield")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("yield")) { attribute.setValue(value); break; attributeSet.add(new EntityAttribute("yield", value)); if (synchSet.contains("passedFiltering")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("passedFiltering")) { attribute.setValue(value); break; attributeSet.add(new EntityAttribute("passedFiltering", value)); if (synchSet.contains("numberOfReads")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("numberOfReads")) { attribute.setValue(value); break; attributeSet.add(new EntityAttribute("numberOfReads", value)); if (synchSet.contains("rawClustersPerLane")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("rawClustersPerLane")) {
attributeNameSet.add(attribute.getName()); EntityAttribute attribute = new EntityAttribute(); attribute.setName(attributeName); attribute.setValue(attributeValue); attributeSet.add(attribute); } else { for (EntityAttribute attribute : attributeSet) { if (attributeName.equals(attribute.getName())) { attribute.setValue(attributeValue);
entityAttributeNameSet.add(attribute.getName()); if (synchSet.contains("observedClusterDensity")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("observedClusterDensity")) { attribute.setValue(value); break; attributeSet.add(new EntityAttribute("observedClusterDensity", value));
attributeNameSet.add(attribute.getName()); EntityAttribute attribute = new EntityAttribute(); attribute.setName(attributeName); attribute.setValue(attributeValue); attributeSet.add(attribute); } else { for (EntityAttribute attribute : attributeSet) { if (attributeName.equals(attribute.getName())) { attribute.setValue(attributeValue);
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();
entityAttributeNameSet.add(attribute.getName()); if (synchSet.contains("PicardMarkDuplicates.readPairDuplicates")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("PicardMarkDuplicates.readPairDuplicates")) { attribute.setValue(readPairDuplicates); break; attributeSet.add(new EntityAttribute("PicardMarkDuplicates.readPairDuplicates", readPairDuplicates)); if (synchSet.contains("PicardMarkDuplicates.percentDuplication")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("PicardMarkDuplicates.percentDuplication")) { attribute.setValue(percentDuplication); break; attributeSet.add(new EntityAttribute("PicardMarkDuplicates.percentDuplication", percentDuplication));
attributeNameSet.add(attribute.getName()); EntityAttribute attribute = new EntityAttribute(); attribute.setName(attributeName); attribute.setValue(attributeValue); attributeSet.add(attribute); } else { for (EntityAttribute attribute : attributeSet) { if (attributeName.equals(attribute.getName())) { attribute.setValue(attributeValue);
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();
entityAttributeNameSet.add(attribute.getName()); if (synchSet.contains("best_match")) { for (EntityAttribute attribute : attributeSet) { if (attribute.getName().equals("best_match")) { attribute.setValue(line.split("\\t")[1]); break; attributeSet.add(new EntityAttribute("best_match", line.split("\\t")[1]));