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

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.

Quantify substitution errors caused by mismatched base pairings during various stages of sample / library prep.

This tool calculates a set of PCR-related metrics from an aligned SAM or BAM file containing targeted sequencing data.

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

Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.

Metrics for evaluating the performance of whole genome sequencing experiments.

A simple program to combine multiple genotyping array VCFs into one VCF The input VCFs must have the same sequence dictionary and same list of variant loci.

Abstract class to facilitate writing command-line programs.

A simple tool to compare two Illumina GTC files.

Rudimentary SAM comparer.

Counting filter that discards reads are unaligned or aligned with MQ==0 and whose 5' ends look like adapter Sequence

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.

Create an Extended Illumina Manifest by performing a liftover to Build 37.

Checks that all data in the set of input files appear to come from the same individual.

Utility class to use with DbSnp files to determine is a locus is a dbSnp site.

Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.

Tools that collect sequencing quality-related and comparative metrics

Simple enum to represent the three possible combinations of major/major, major/minor and minor/minor haplotypes for a diploid individual.

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

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 scheme is defined in the constructor.

Concatenate efficiently BAM files that resulted from a scattered parallel analysis.

Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.

Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.

Utilities to calculate GC Bias Created by kbergin on 9/23/15.

Load gene annotations into an OverlapDetector of Gene objects.

A simple structure to return the results of getAlleles.

A class to store the counts for various truth and call state classifications relative to a reference.

This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.

Created by kbergin on 7/30/15.

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

A minute class to store the truth and call state respectively.

Class that holds summary metrics about Genotype Concordance

Genotype filter that filters out genotypes below a given quality threshold.

Created by farjoun on 11/2/16.

Class to convert an Illumina GTC file into a VCF file.

Represents information about a group of SNPs that form a haplotype in perfect LD with one another.

Abstract class for storing and calculating various likelihoods and probabilities for haplotype alleles given evidence.

Represents the probability of the underlying haplotype of the contaminating sample given the data.

Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood) for each of the SNPs in that block.

A wrapper class for any HaplotypeProbabilities instance that will assume that the given evidence is that of a tumor sample and provide an hp for the normal sample that tumor came from.

Calculates HS metrics for a given SAM or BAM file.

Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.

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

A simple class to represent a locus entry in an Illumina Bead Pool Manifest (BPM) file

List of data types of interest when parsing Illumina data.

Embodies characteristics that describe a lane.

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

Illumina's TileMetricsOut.bin file codes various metrics, both concrete (all density id's are code 100) or as a base code (e.g.

A read name encoder following the encoding initially produced by picard fastq writers.

Describes adapters used on each pair of strands

Metric to be used for InDel errors

A class to provide methods for accessing Illumina Infinium Data Files.

A class to encapsulate the table of contents for an Illumina Infinium Data Files.

Collects InsertSizeMetrics on the specified accumulationLevels using

Base interface for an interval argument collection.

An interface for a class that scatters IntervalLists.

Scatters IntervalList by interval count so that resulting IntervalList's have the same number of intervals in them.

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

Liftover SNPs in HaplotypeMaps from one reference to another

Created by jcarey on 3/13/14.

Describes the behavior of a locus relative to a gene.

Creates a TSV from sample name to VCF/GVCF path, with one line per input.

Enum used to control how duplicates are flagged in the DT optional tag on each read.

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