All Classes

Class for parsing text files where each line consists of fields separated by whitespace.

Little class used to package up a header and an iterable/iterator.

Class for collecting data on reference coverage, base qualities and excluded bases from one AbstractLocusInfo object for CollectWgsMetrics.

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.

Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be efficient.

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.

Class to take unmapped reads in BAM file format and create Maq binary fastq format file(s) -- one or two of them, depending on whether it's a paired-end read.

Reads a single barcode file line by line and returns the barcode if there was a match or NULL otherwise.

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

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

Created by jcarey on 3/14/14.

Describes a mechanism for revising and evaluating qualities read from a BCL file.

This strategy was designed for TopHat output, but could be of general utility.

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

Collects variants and generates metrics about them.

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.

Tool to collect information about GC bias in the reads in a given BAM file.

a metric class for describing FP failing reads from an Illumina HiSeqX lane *

This tool takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection.

Command-line wrapper around CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.

A CLP that, given a BAM and a VCF with genotypes of the same sample, estimates the rate of independent replication of reads within the bam.

Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.

Class for trying to quantify the CpCG->CpCA error rate.

Command line program to calibrate quality yield metrics

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).

Metrics for evaluating the performance of whole genome sequencing experiments.

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.

Rudimentary SAM comparer.

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

A SamRecordFilter that counts the number of bases in the reads which it filters out.

Counting filter that discards reads that are unpaired in sequencing and paired reads whose mates are not mapped.

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.

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

Created by farjoun on 6/26/18.

Attempts to estimate library complexity from sequence alone.

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.

Utility class to hang onto data about the best match for a given barcode

Converts a FASTQ file to an unaligned BAM or SAM file.

Summary

Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying iterator.

Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not.

Summary

Major class that coordinates the activities involved in comparing genetic fingerprint data whether the source is from a genotyping platform or derived from sequence data.

Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.

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

Holds a 4 short values for each cycle of a read.

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 totally discrete 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.

Created by farjoun on 11/2/16.

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.

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

IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM or BAM file format.

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.

Embodies characteristics that describe a lane.

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 class to store information relevant for biological rate estimation

Collects InsertSizeMetrics on the specified accumulationLevels using

Base interface for an interval argument collection.

a Baseclass for scatterers that scatter by uniqued base count.

A BaseCount Scatterer that avoid breaking-up intervals.

An IntervalListScatterer that attempts to place the same number of (uniquified) bases in each output interval list.

Trivially simple command line program to convert an IntervalList file to a BED file.

Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics

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.

This will iterate through a coordinate sorted SAM file (iterator) and either mark or remove duplicates as appropriate.

This is the mark queue.

General math utilities

Program to generate a data table and chart of mean quality by cycle from a BAM file.

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.

This tool is used for combining SAM and/or BAM files from different runs or read groups into a single file, similar to the \"merge\" function of Samtools (http://www.htslib.org/doc/samtools.html).

For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.

For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size.

NextSeq-style bcl's have all tiles for a cycle in a single file.

For file types for which there is one file per lane, with fixed record size, and all the tiles in it, so the s_.bci file can be used to figure out where each tile starts and ends.

Created by jcarey on 3/13/14.

Abstract class for files with fixed-length records for multiple tiles, e.g.

Parse cbcls Illumina Basecall files, and use them the to populate ClusterData objects.

Little program to "normalize" a fasta file to ensure that all line of sequence are the same length, and are a reasonable length!

Picard default argument collection for an optional reference.

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.

Represents a .ped file of family information as documented here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml Stores the information in memory as a map of individualId -> Pedigree information for that individual

Argument Collection which holds parameters common to classes that want to add PG tags to reads in SAM/BAM files

Stores the minimal information needed for optical duplicate detection.

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

This is the main class of Picard and is the way of executing individual command line programs.

Custom Barclay-based Javadoc Doclet used for generating Picard help/documentation.

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.

Utility for loading properties files from resources.

Charts quality score distribution within a BAM file.

Classes, methods, and enums that deal with the stratification of read bases and reference information.

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 according to the overall mismatches (from 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 for holding the direction for a read (positive strand or negative strand

The main interface for a stratifier.

Tools that manipulate read data in SAM, BAM or CRAM format

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

Codec for ReadEnds that just outputs the primitive fields and reads them back.

A class to store individual records for MarkDuplicatesWithMateCigar.

Provides access to the physical location information about a cluster.

A read type describes a stretch of cycles in an ReadStructure (e.g.

Tools that analyze and manipulate FASTA format references

Renames a sample within a VCF or BCF.

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

Argument collection for references that are required (and not common).

Used as a return for the canSkipSAMFile function.

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".

Class that takes in a set of alignment information in SAM format and merges it with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.

Defines a MultilevelPerRecordCollector using the argument type of SAMRecord so that this doesn't have to be redefined for each subclass of MultilevelPerRecordCollector

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.

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.

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.

Sorts a SAM or BAM file.

Command-line program to split a SAM or BAM file into separate files based on library name.

Splits the input VCF file into two, one for indels and one for SNPs.

Parser for tab-delimited files

Metrics class for the analysis of reads obtained from targeted pcr experiments e.g.

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.

Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.

A VariantAccumulatorExecutor that breaks down work into chunks described by the provided VariantIteratorProducer and spreads them over the indicated number of threads.

Interface for classes that can generate filters for VariantContexts.

A mechanism for iterating over CloseableIterator of VariantContexts in in some fashion, given VCF files and optionally an interval list.

Describes an object that processes variants and produces a result.

Generates instances of VariantProcessor.Accumulators.

Takes a collection of results produced by VariantProcessor.Accumulator.result() and merges them into a single RESULT.

Describes a segment of a particular VCF file.

Converts an ASCII VCF file to a binary BCF or vice versa.

Created by farjoun on 4/1/17.

Interface for processing data and generate result for CollectWgsMetrics