# Package picard.analysis

- Interface Summary
  Interface | Description
  --- | ---
  CollectMultipleMetrics.ProgramInterface |
  WgsMetricsProcessor | Interface for processing data and generate result for CollectWgsMetrics

- Class Summary
  Class | Description
  --- | ---
  AbstractWgsMetricsCollector<T extends htsjdk.samtools.util.AbstractRecordAndOffset> | Class for collecting data on reference coverage, base qualities and excluded bases from one AbstractLocusInfo object for CollectWgsMetrics.
  AdapterUtility | A utility class for matching reads to adapters.
  AlignmentSummaryMetrics | High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
  AlignmentSummaryMetricsCollector |
  BaseDistributionByCycleMetrics |
  ChimeraUtil |
  CollectAlignmentSummaryMetrics | A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
  CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection |
  CollectBaseDistributionByCycle |
  CollectGcBiasMetrics | Tool to collect information about GC bias in the reads in a given BAM file.
  CollectInsertSizeMetrics | Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.
  CollectJumpingLibraryMetrics | Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.
  CollectMultipleMetrics | Class that is designed to instantiate and execute multiple metrics programs that extend SinglePassSamProgram while making only a single pass through the SAM file and supplying each program with the records as it goes.
  CollectOxoGMetrics | Class for trying to quantify the CpCG->CpCA error rate.
  CollectOxoGMetrics.CpcgMetrics | Metrics class for outputs.
  CollectQualityYieldMetrics | Command line program to calculate quality yield metrics
  CollectQualityYieldMetrics.QualityYieldMetrics | A set of metrics used to describe the general quality of a BAM file
  CollectQualityYieldMetrics.QualityYieldMetricsCollector |
  CollectRawWgsMetrics | Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, same implementation as `CollectWgsMetrics`, with different defaults: lacks baseQ and mappingQ filters and has much higher coverage cap.
  CollectRawWgsMetrics.RawWgsMetrics |
  CollectRnaSeqMetrics |
  CollectRrbsMetrics | Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well as CpG sites across all reads in the input BAM/SAM file.
  CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection |
  CollectWgsMetrics | Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
  CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection |
  CollectWgsMetrics.WgsMetricsCollector |
  CollectWgsMetricsWithNonZeroCoverage |
  CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage | Metrics for evaluating the performance of whole genome sequencing experiments.
  CompareMetrics | Compare two metrics files.
  CounterManager | Class for managing a list of Counters of integer, provides methods to access data from Counters with respect to an offset.
  FastWgsMetricsCollector | Class represents fast algorithm for collecting data from `AbstractLocusInfo` with a list of aligned `EdgingRecordAndOffset` objects.
  FingerprintingDetailMetrics | Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
  FingerprintingSummaryMetrics | Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs.
  GcBiasDetailMetrics | Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
  GcBiasMetricsCollector | Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.
  GcBiasSummaryMetrics | High level metrics that capture how biased the coverage in a certain lane is.
  GcBiasUtils | Utilities to calculate GC Bias Created by kbergin on 9/23/15.
  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 ".insert_size_metrics".
  JumpingLibraryMetrics | High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".
  MeanQualityByCycle | Program to generate a data table and chart of mean quality by cycle from a BAM file.
  MergeableMetricBase | An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated (`MergeByAdding`).
  QualityScoreDistribution | Charts quality score distribution within a BAM file.
  RnaSeqMetrics | Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".
  RrbsCpgDetailMetrics | Holds information about CpG sites encountered for RRBS processing QC
  RrbsMetricsCollector |
  RrbsSummaryMetrics | Holds summary statistics from RRBS processing QC
  SinglePassSamProgram | Super class that is designed to provide some consistent structure between subclasses that simply iterate once over a coordinate sorted BAM and collect information from the records as the go in order to produce some kind of output.
  TheoreticalSensitivity | Created by David Benjamin on 5/13/15.
  TheoreticalSensitivity.RouletteWheel |
  TheoreticalSensitivityMetrics | TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in the calculation.
  WgsMetrics | Metrics for evaluating the performance of whole genome sequencing experiments.
  WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset> | Implementation of `WgsMetricsProcessor` that gets input data from a given iterator and processes it with a help of collector

- Enum Summary
  Enum | Description
  --- | ---
  AlignmentSummaryMetrics.Category |
  CollectMultipleMetrics.Program |
  CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category |
  MetricAccumulationLevel | For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.

- Annotation Types Summary
  Annotation Type | Description
  --- | ---
  MergeableMetricBase.MergeByAdding | Metrics whose values can be merged by adding.
  MergeableMetricBase.MergeByAssertEquals | Metrics whose values should be equal when merging.
  MergeableMetricBase.MergingIsManual | Metrics that are merged manually in the `MergeableMetricBase.merge(MergeableMetricBase)` ()}.
  MergeableMetricBase.NoMergingIsDerived | Metrics that are not merged, but are subsequently derived from other metrics, for example by `MergeableMetricBase.calculateDerivedFields()`.
  MergeableMetricBase.NoMergingKeepsValue | Metrics that are not merged.