| Interface | Description |
|---|---|
| PerUnitMetricCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.Comparable<HKEY>,ARGTYPE> |
PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.
|
| Class | Description |
|---|---|
| InsertSizeMetrics |
Metrics 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".
|
| InsertSizeMetricsArgumentCollection |
ArgumentCollection for InsertSizeMetrics collectors.
|
| InsertSizeMetricsCollector |
Collects InsertSizeMetrics on the specified accumulationLevels
|
| MetricsArgumentCollection |
Base class for defining a set of metrics collector arguments.
|
| MetricsUtils |
Utility methods for dealing with
MetricsFile and related classes. |
| MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,HISTOGRAM_KEY extends java.lang.Comparable<HISTOGRAM_KEY>,ARGTYPE> |
MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).
|
| MultiLevelMetrics | |
| MultiLevelReducibleCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,HISTOGRAM_KEY extends java.lang.Comparable<HISTOGRAM_KEY>,ARGTYPE,UNIT_COLLECTOR extends PerUnitMetricCollector<METRIC_TYPE,HISTOGRAM_KEY,ARGTYPE>> |
Abstract base class for reducible multi-level metrics collectors.
|
| PerUnitInsertSizeMetricsCollector |
A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or
SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)
|
| QualityYieldMetrics |
A set of metrics used to describe the general quality of a BAM file
|
| QualityYieldMetricsArgumentCollection |
MetricsArgumentCollection argument collection for QualityYield metrics.
|
| SAMRecordAndReference | |
| SAMRecordAndReferenceMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.Comparable<HKEY>> | |
| SAMRecordMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.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
|
| Enum | Description |
|---|---|
| MetricAccumulationLevel |
For use with Picard metrics programs that may output metrics for multiple levels
of aggregation with an analysis.
|