All Classes

Abstract class that coordinates the general task of taking in a set of alignment information, possibly in SAM format, possibly in other formats, and merging that with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.

The position files of Illumina are nearly the same form: Pos files consist of text based tabbed x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary x-y float pairs.

Abstract class that holds parameters and methods common to classes that perform duplicate detection and/or marking within SAM/BAM/CRAM files.

Abstract class that holds parameters and methods common to classes that optical duplicate detection.

Combines multiple Picard QualityYieldMetrics files into a single file.

Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.

A utility class for matching reads to adapters.

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".

Utilities class containing methods for restricting VariantContext and GenotypesContext objects to a reduced set of alleles, as well as for choosing the best set of alleles to keep and for cleaning up annotations and genotypes after subsetting.

A simple class to store names and counts for the the Control Information fields that are stored in an Illumina GTC file.

Describes

Designs baits for hybrid selection!

Command line program to print statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate.

BarcodeExtractor is used to match barcodes and collect barcode match metrics.

Created by jcarey on 3/13/14.

Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.

An interface that can take a collection of bases (provided as SamLocusIterator.RecordAndOffset and SamLocusAndReferenceIterator.SAMLocusAndReference) and generates a ErrorMetric from them.

BasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).

Interface that defines a writer that will write out OUTPUT_RECORD type objects.

Parse various formats and versions of Illumina Basecall files, and use them the to populate ClusterData objects.

Created by jcarey on 3/14/14.

Annoyingly, there are two different files with extension .bci in NextSeq output.

BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters.

For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary.

A simple program to convert an Illumina bpm (bead pool manifest file) into a normalization manifest (bpm.csv) file The normalization manifest (bpm.csv) is a simple text file generated by Illumina tools - it has a specific format and is used by ZCall .

A class to represent a record (line) from an Extended Illumina Manifest [Assay] entry

Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals.

A read name encoder conforming to the standard described by Illumina Casava 1.8.

------------------------------------- CBCL Header ----------------------------------- Bytes 0 - 1 Version number, current version is 1 unsigned 16 bits little endian integer Bytes 2 - 5 Header size unsigned 32 bits little endian integer Byte 6 Number of bits per basecall unsigned Byte 7 Number of bits per q-score unsigned

Program to check a lane of an Illumina output directory.

Utility class that can scan for classes in the classpath and find all the ones annotated with a particular annotation.

Utilities to clip the adapter sequence from a SAMRecord read

The clocs file format is one of 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.

Store the information from Illumina files for a single cluster with one or more reads.

A metric class to hold the result of ClusterCrosscheckMetrics fingerprints.

Collect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.

Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter.

Metrics produced by the GetHiSeqXPFFailMetrics program.

A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect.

Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.

Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.

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.

Metrics class for outputs.

A set of metrics used to describe the general quality of a BAM file

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.

Program to collect error metrics on bases stratified in various ways.

Both CollectTargetedPCRMetrics and CollectHsSelection share virtually identical program structures except for the name of their targeting mechanisms (e.g.

Collects summary and per-sample metrics about variant calls in a VCF file.

A collection of metrics relating to snps and indels within a variant-calling file (VCF).

Embodies defaults for global values that affect how the Picard Command Line operates.

Class for handling translation of Picard-style command line argument syntax to POSIX-style argument syntax; used for running tests written with Picard style syntax against the Barclay command line parser.

Compare two metrics files.

Class for managing a list of Counters of integer, provides methods to access data from Counters with respect to an offset.

Counting filter that discards reads that have been marked as duplicates.

Counting filter that discards reads below a configurable mapping quality threshold.

A simple program to create a standard picard metrics file from the output of bafRegress

Create a SAM/BAM file from a fasta containing reference sequence.

A simple program to create a standard picard metrics file from the output of VerifyIDIntensity

A class to hold the result of crosschecking fingerprints.

Little tuple class to contain one bitset for SNPs and another for Indels.

Filters out a record if all variant samples have depth lower than the given value.

A genotype produced by one of the concrete implementations of AbstractAlleleCaller.

Disk-based implementation of ReadEndsForMarkDuplicatesMap.

Summary

Factory class that creates either regular or flow-based duplication metrics.

Summary metrics produced by CollectSequencingArtifactMetrics as a roll up of the context-specific error rates, to provide global error rates per type of base substitution.

Determine the barcode for each read in an Illumina lane.

Simple command line program that allows sub-sequences represented by an interval list to be extracted from a reference sequence file.

Class represents fast algorithm for collecting data from AbstractLocusInfo with a list of aligned EdgingRecordAndOffset objects.

Created by jcarey on 3/13/14.

Summary

Applies a set of hard filters to Variants and to Genotypes within a VCF.

class to represent a genetic fingerprint as a set of HaplotypeProbabilities objects that give the relative probabilities of each of the possible haplotypes at a locus.

class to hold the details of a element of fingerprinting PU tag

Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs.

Class that is used to represent the results of comparing a read group within a SAM file, or a sample within a VCF against one or more set of fingerprint genotypes.

A class that holds VariantContexts sorted by genomic position

Summary

The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.

Simple little class that combines multiple VCFs that have exactly the same set of samples and nonoverlapping sets of loci.

High level metrics that capture how biased the coverage in a certain lane is.

Holds annotation of a gene for storage in an OverlapDetector.

Summary

Class that holds metrics about the Genotype Concordance contingency tables.

Class that holds detail metrics about Genotype Concordance

Created by kbergin on 6/19/15.

A class to store the various classifications for: 1.

A specific state for a 2x2 contingency table.

These states represent the relationship between a truth genotype and the reference sequence.

An interface for classes that perform Genotype filtration.

Miscellaneous tools, e.g.

An accumulator for collecting metrics about a single-sample GVCF.

A collection of metadata about Haplotype Blocks including multiple in memory "indices" of the data to make it easy to query the correct HaplotypeBlock or Snp by snp names, positions etc.

Log10(P(evidence| haplotype)) for the 3 different possible haplotypes {aa, ab, bb}

Represents a set of HaplotypeProbabilities that were derived from a single SNP genotype at a point in time.

Represents the probability of the underlying haplotype given the data.

Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments.

A class to encompass writing an Illumina adpc.bin file.

Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.

Simple switch to control the read name format to emit.

A class to parse the contents of an Illumina Bead Pool Manifest (BPM) file A BPM file contains metadata (including the alleles, mapping and normalization information) on an Illumina Genotyping Array Each type of genotyping array has a specific BPM .

IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.

General utils for dealing with IlluminaFiles as well as utils for specific, support formats.

A class to represent an Illumina Manifest file.

Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.

Misc utilities for working with Illumina specific files and data

A calculator that estimates the error rate of the bases it observes for indels only.

A class to store information relevant for biological rate estimation

A class to parse the contents of an Illumina Infinium cluster (EGT) file A cluster file contains information about the clustering information used in mapping red / green intensity information to genotype calls

A class to parse the contents of an Illumina Infinium genotype (GTC) file A GTC file is the output of Illumina's genotype calling software (either Autocall or Autoconvert) and contains genotype calls, confidence scores, basecalls and raw intensities for all calls made on the chip.

A class to parse the contents of an Illumina Infinium Normalization Manifest file An Illumina Infinium Normalization Manifest file contains a subset of the information contained in the Illumina Manifest file in addition to the normalization ID which is needed for normalizating intensities in GtcToVcf

A class to store fields that are specific to a VCF generated from an Illumina GTC file.

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".

The channels in a FourChannelIntensityData object, and the channels produced by a ClusterIntensityFileReader, for cases in which it is desirable to handle these abstractly rather than having the specific names in the source code.

a Baseclass for scatterers that scatter by uniqued base count.

Scatters IntervalList by into `interval count` shards so that resulting IntervalList's have approximately same number of intervals in them.

Like IntervalListScattererWithoutSubdivision but will overflow current list if the projected size of the remaining lists is bigger than the "ideal".

An enum to control the creation of the various IntervalListScatter objects

Performs various IntervalList manipulations.

Tools that process genomic intervals in various formats.

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".

A class to generate library Ids and keep duplication metrics by library IDs.

This tool adjusts the coordinates in an interval list on one reference to its homologous interval list on another reference, based on a chain file that describes the correspondence between the two references.

Summary

The locs file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.

Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.

A better duplication marking algorithm that handles all cases including clipped and gapped alignments.

Enum for the possible values that a duplicate read can be tagged with in the DT attribute.

MarkDuplicates calculation helper class for flow based mode The class extends the behavior of MarkDuplicates which contains the complete code for the non-flow based mode.

An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.

Command line program to mark the location of adapter sequences.

Represents the results of a fingerprint comparison between one dataset and a specific fingerprint file.

A collection of common math operations that work with log values.

Map from String to ReadEnds object.

Created by farjoun on 6/25/16.

Metrics whose values can be merged by adding.

Metrics that are merged manually in the MergeableMetricBase.merge(MergeableMetricBase) ()}.

Metrics that are not merged.

Class to take genotype calls from a ped file output from zCall and merge them into a vcf from autocall.

Combines multiple variant files into a single variant file.

MMapBackedIteratorFactory a file reader that takes a header size and a binary file, maps the file to a read-only byte buffer and provides methods to retrieve the header as it's own bytebuffer and create iterators of different data types over the values of file (starting after the end of the header).

MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).

Created by jcarey on 3/13/14.

Parse .bcl.bgzf files that contain multiple tiles in a single file.

Read filter file that contains multiple tiles in a single file.

Read locs file that contains multiple tiles in a single file.

A tool to count the number of non-N bases in a fasta file

Contains methods for finding optical/co-localized/sequencing duplicates.

Miscellaneous tools, e.g.

In multiple locations we need to know what cycles are output, as of now we output all non-skip cycles, but rather than sprinkle this knowledge throughout the parser code, instead OutputMapping provides all the data a client might want about the cycles to be output including what ReadType they are.

A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.

An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem.

A base class for Metrics for targeted panels.

A class whose purpose is to initialize the various plugins that provide Path support.

Abstract base class for Parsers that open a single tile file at a time and iterate through them.

PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.

Small interface that provides access to the physical location information about a cluster.

This stores records that are comparable for detecting optical duplicates.

Small class that provides access to the physical location information about a cluster.

Basic Picard runtime exception that, for now, does nothing much

Created by jcarey on 3/13/14.

Summary

Performs on-the-fly filtering of the provided VariantContext Iterator such that only variants that satisfy all predicates are emitted.

Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate.

Filters out sites that have a QD annotation applied to them and where the QD value is lower than a lower limit.

A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairs

While structurally identical to CompositeIndex, this class is maintained as it makes code more readable when the two are used together (see QSeqParser)

Stratifies into quintiles of read cycle.

A CollectionStratifier is a stratifier that uses a collection of stratifiers to inform the stratification.

Stratify by tags used during duplex and single index consensus calling.

Stratifies base into their read's tile which is parsed from the read-name.

Stratifies base into their read's Y coordinate which is parsed from the read-name.

Stratifies according to the length of an insertion or deletion.

Stratifies according to the overall mismatches (from SAMTag.NM) that the read has against the reference, NOT including the current base.

An enum for holding a reads read-pair's Orientation (i.e.

An enum to hold information about the "properness" of a read pair

An enum to hold the ordinality of a read

Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.

Represents one set of cycles in an ReadStructure (e.g.

Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar

Interface for storing and retrieving ReadEnds objects.

Created by nhomer on 9/13/15.

Describes the intended logical output structure of clusters of an Illumina run.

Base interface for a reference argument collection.

Loads gene annotations from a refFlat file into an OverlapDetector.

Class which contains utility functions that use reflection.

Reorders a SAM/BAM input file according to the order of contigs in a second reference file.

Little struct-like class to hold a record index, the index of the corresponding representative read, and duplicate set size information.

This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped SAM, BAM or CRAM files.

Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.

Util class for executing R scripts.

Holds information about CpG sites encountered for RRBS processing QC

Holds summary statistics from RRBS processing QC

Compare two SAM/BAM files.

Argument collection for SAM comparison

Converts a BAM file to human-readable SAM output or vice versa

This class sets the duplicate read flag as the result state when examining sets of records.

Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger FASTQ format.

A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.

Class with helper methods for generating and writing SequenceDictionary objects.

Summary analysis of a single bait bias artifact, also known as a reference bias artifact.

Summary analysis of a single pre-adapter artifact.

Fixes the NM, MD, and UQ tags in a SAM or BAM file.

A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.

A class for finding the distance between a single barcode and a barcode-read (with base qualities)

Class to represent a SNP in context of a haplotype block that is used in fingerprinting.

Summary

Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate.

Splits the input queryname sorted or query-grouped SAM/BAM/CRAM file and writes it into multiple BAM files, each with an approximately equal number of reads.

A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.

Parse a tabbed text file in which columns are found by looking at a header line rather than by position.

Calculates HS metrics for a given SAM or BAM file.

TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).

A simple class that is used to store the coverage information about an interval.

For internal test purposes only.

Represents a tile from TileMetricsOut.bin.

Helper class which captures the combination of a lane, tile & metric code

Captures information about a phasing value - Which read it corresponds to, which phasing type and a median value

Enum representation of a transition from one base to any other.

This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.

Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.

UnortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).

This tool reports on the validity of a SAM or BAM file relative to the SAM format specification.

Describes the functionality for an executor that manages the delegation of work to VariantProcessor.Accumulators.

Tools that evaluate and refine variant calls, e.g.

Tools that filter variants

Tools that manipulate variant call format (VCF) data

Handles VariantContexts, and accumulates their data in some fashion internally.

Simple builder of VariantProcessors.

Enum to hold the possible types of dbSnps.

Describes a segment of a particular VCF file.

A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).

Metrics for evaluating the performance of whole genome sequencing experiments.

Implementation of WgsMetricsProcessor that gets input data from a given iterator and processes it with a help of collector