Searched refs:accumulationLevels (Results 1 – 9 of 9) sorted by relevance
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/ |
| H A D | InsertSizeMetricsCollectorSparkUnitTest.java | 76 isArgs.metricAccumulationLevel.accumulationLevels = new HashSet<>(); in test()
77 … isArgs.metricAccumulationLevel.accumulationLevels.add(MetricAccumulationLevel.ALL_READS); in test()
78 isArgs.metricAccumulationLevel.accumulationLevels.add(MetricAccumulationLevel.SAMPLE); in test()
79 isArgs.metricAccumulationLevel.accumulationLevels.add(MetricAccumulationLevel.LIBRARY); in test()
80 … isArgs.metricAccumulationLevel.accumulationLevels.add(MetricAccumulationLevel.READ_GROUP); in test()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/metrics/ |
| H A D | MultiLevelReducibleCollectorUnitTest.java | 113 final Set<MetricAccumulationLevel> accumulationLevels, in RecordCountMultiLevelCollector() argument
115 setup(accumulationLevels, samRgRecords); in RecordCountMultiLevelCollector()
211 public void multilevelCollectorTest(final Set<MetricAccumulationLevel> accumulationLevels) { in multilevelCollectorTest() argument
215 accumulationLevels, in.getFileHeader().getReadGroups()); in multilevelCollectorTest()
217 accumulationLevels, in.getFileHeader().getReadGroups()); in multilevelCollectorTest()
238 for(final MetricAccumulationLevel level : accumulationLevels) { in multilevelCollectorTest()
|
| H A D | MultiLevelCollectorTest.java | 58 …public RecordCountMultiLevelCollector(final Set<MetricAccumulationLevel> accumulationLevels, final… in RecordCountMultiLevelCollector() argument
59 setup(accumulationLevels, samRgRecords); in RecordCountMultiLevelCollector()
166 public void multilevelCollectorTest(final Set<MetricAccumulationLevel> accumulationLevels) { in multilevelCollectorTest() argument
168 …MultiLevelCollector collector = new RecordCountMultiLevelCollector(accumulationLevels, in.getFileH… in multilevelCollectorTest()
178 for(final MetricAccumulationLevel level : accumulationLevels) { in multilevelCollectorTest()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/metrics/ |
| H A D | MultiLevelCollector.java | 261 …protected void setup(final Set<MetricAccumulationLevel> accumulationLevels, final List<SAMReadGrou… in setup() argument
263 if(accumulationLevels.contains(MetricAccumulationLevel.ALL_READS)) { in setup()
266 if (accumulationLevels.contains(MetricAccumulationLevel.SAMPLE)) { in setup()
270 if(accumulationLevels.contains(MetricAccumulationLevel.LIBRARY)) { in setup()
274 if(accumulationLevels.contains(MetricAccumulationLevel.READ_GROUP)) { in setup()
|
| H A D | MultiLevelReducibleCollector.java | 429 …protected void setup(final Set<MetricAccumulationLevel> accumulationLevels, final List<SAMReadGrou… in setup() argument
431 if(accumulationLevels.contains(MetricAccumulationLevel.ALL_READS)) { in setup()
437 if (accumulationLevels.contains(MetricAccumulationLevel.SAMPLE)) { in setup()
444 if(accumulationLevels.contains(MetricAccumulationLevel.LIBRARY)) { in setup()
451 if(accumulationLevels.contains(MetricAccumulationLevel.READ_GROUP)) { in setup()
|
| H A D | InsertSizeMetricsCollector.java | 51 setup(inputArgs.metricAccumulationLevel.accumulationLevels, samHeader.getReadGroups()); in initialize()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/ |
| H A D | CollectMultipleMetricsSpark.java | 123 isArgs.metricAccumulationLevel.accumulationLevels = metricAccumulationLevel; in createCollector()
180 metricAccumulationLevel.accumulationLevels, in runTool()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/ |
| H A D | MetricAccumulationLevelArgumentCollection.java | 21 …public Set<MetricAccumulationLevel> accumulationLevels = EnumSet.of(MetricAccumulationLevel.ALL_RE… field in MetricAccumulationLevelArgumentCollection
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/examples/metrics/multi/ |
| H A D | ExampleMultiMetricsCollector.java | 52 setup(inputArgs.metricAccumulationLevel.accumulationLevels, samHeader.getReadGroups()); in initialize()
|