picard.analysis

Interfaces

• CollectMultipleMetrics.ProgramInterface
• WgsMetricsProcessor

Classes

• AbstractWgsMetricsCollector
• AdapterUtility
• AlignmentSummaryMetrics
• AlignmentSummaryMetricsCollector
• BaseDistributionByCycleMetrics
• ChimeraUtil
• CollectAlignmentSummaryMetrics
• CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
• CollectBaseDistributionByCycle
• CollectGcBiasMetrics
• CollectInsertSizeMetrics
• CollectJumpingLibraryMetrics
• CollectMultipleMetrics
• CollectOxoGMetrics
• CollectOxoGMetrics.CpcgMetrics
• CollectQualityYieldMetrics
• CollectQualityYieldMetrics.QualityYieldMetrics
• CollectQualityYieldMetrics.QualityYieldMetricsCollector
• CollectRawWgsMetrics
• CollectRawWgsMetrics.RawWgsMetrics
• CollectRnaSeqMetrics
• CollectRrbsMetrics
• CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
• CollectWgsMetrics
• CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
• CollectWgsMetrics.WgsMetrics
• CollectWgsMetrics.WgsMetricsCollector
• CollectWgsMetricsWithNonZeroCoverage
• CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
• CompareMetrics
• CounterManager
• FastWgsMetricsCollector
• FingerprintingDetailMetrics
• FingerprintingSummaryMetrics
• GcBiasDetailMetrics
• GcBiasMetricsCollector
• GcBiasSummaryMetrics
• GcBiasUtils
• InsertSizeMetrics
• JumpingLibraryMetrics
• MeanQualityByCycle
• MergeableMetricBase
• QualityScoreDistribution
• RnaSeqMetrics
• RrbsCpgDetailMetrics
• RrbsMetricsCollector
• RrbsSummaryMetrics
• SinglePassSamProgram
• TheoreticalSensitivity
• TheoreticalSensitivity.RouletteWheel
• WgsMetricsProcessorImpl

Enums

• AlignmentSummaryMetrics.Category
• CollectMultipleMetrics.Program
• CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
• MetricAccumulationLevel

Annotation Types

• MergeableMetricBase.MergeByAdding
• MergeableMetricBase.MergeByAssertEquals
• MergeableMetricBase.MergingIsManual
• MergeableMetricBase.NoMergingIsDerived
• MergeableMetricBase.NoMergingKeepsValue