Package org.broadinstitute.hellbender.metrics
package org.broadinstitute.hellbender.metrics
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ClassDescriptionMetrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insertSizeMetrics".ArgumentCollection for InsertSizeMetrics collectors.Collects InsertSizeMetrics on the specified accumulationLevelsFor use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.Base class for defining a set of metrics collector arguments.Utility methods for dealing with
MetricsFileand related classes.MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,HISTOGRAM_KEY extends Comparable<HISTOGRAM_KEY>, ARGTYPE> MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).MultiLevelReducibleCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,HISTOGRAM_KEY extends Comparable<HISTOGRAM_KEY>, ARGTYPE, UNIT_COLLECTOR extends PerUnitMetricCollector<METRIC_TYPE, HISTOGRAM_KEY, ARGTYPE>> Abstract base class for reducible multi-level metrics collectors.A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)PerUnitMetricCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends Comparable<HKEY>, ARGTYPE> PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.A set of metrics used to describe the general quality of a BAM fileMetricsArgumentCollection argument collection for QualityYield metrics.SAMRecordAndReferenceMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends Comparable<HKEY>> SAMRecordMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends Comparable<HKEY>> Defines a MultilevelPerRecordCollector using the argument type of SAMRecord so that this doesn't have to be redefined for each subclass of MultilevelPerRecordCollector