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.
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AdapterUtility |
A utility class for matching reads to adapters.
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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".
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AlignmentSummaryMetricsCollector |
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BaseDistributionByCycleMetrics |
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ChimeraUtil |
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CollectAlignmentSummaryMetrics |
A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
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CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection |
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CollectBaseDistributionByCycle |
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CollectGcBiasMetrics |
Tool to collect information about GC bias in the reads in a given BAM file.
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CollectInsertSizeMetrics |
Command line program to read non-duplicate insert sizes, create a Histogram
and report distribution statistics.
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CollectJumpingLibraryMetrics |
Command-line program to compute metrics about outward-facing pairs, inward-facing
pairs, and chimeras in a jumping library.
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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.
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CollectOxoGMetrics |
Class for trying to quantify the CpCG->CpCA error rate.
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CollectOxoGMetrics.CpcgMetrics |
Metrics class for outputs.
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CollectQualityYieldMetrics |
Command line program to calibrate quality yield metrics
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CollectQualityYieldMetrics.QualityYieldMetrics |
A set of metrics used to describe the general quality of a BAM file
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CollectQualityYieldMetrics.QualityYieldMetricsCollector |
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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.
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CollectRawWgsMetrics.RawWgsMetrics |
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CollectRnaSeqMetrics |
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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.
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CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection |
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CollectWgsMetrics |
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
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CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection |
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CollectWgsMetrics.WgsMetricsCollector |
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CollectWgsMetricsWithNonZeroCoverage |
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CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage |
Metrics for evaluating the performance of whole genome sequencing experiments.
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CompareMetrics |
Compare two metrics files.
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CounterManager |
Class for managing a list of Counters of integer,
provides methods to access data from Counters with respect to an offset.
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FastWgsMetricsCollector |
Class represents fast algorithm for collecting data from AbstractLocusInfo
with a list of aligned EdgingRecordAndOffset objects.
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FingerprintingDetailMetrics |
Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
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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.
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GcBiasDetailMetrics |
Class that holds detailed metrics about reads that fall within windows of a certain
GC bin on the reference genome.
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GcBiasMetricsCollector |
Calculates GC Bias Metrics on multiple levels
Created by kbergin on 3/23/15.
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GcBiasSummaryMetrics |
High level metrics that capture how biased the coverage in a certain lane is.
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GcBiasUtils |
Utilities to calculate GC Bias
Created by kbergin on 9/23/15.
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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".
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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".
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MeanQualityByCycle |
Program to generate a data table and chart of mean quality by cycle from a
BAM file.
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MergeableMetricBase |
An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated ( MergeByAdding ).
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QualityScoreDistribution |
Charts quality score distribution within a BAM file.
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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".
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RrbsCpgDetailMetrics |
Holds information about CpG sites encountered for RRBS processing QC
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RrbsMetricsCollector |
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RrbsSummaryMetrics |
Holds summary statistics from RRBS processing QC
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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.
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TheoreticalSensitivity |
Created by David Benjamin on 5/13/15.
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TheoreticalSensitivity.RouletteWheel |
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TheoreticalSensitivityMetrics |
TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in
the calculation.
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WgsMetrics |
Metrics for evaluating the performance of whole genome sequencing experiments.
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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
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