gngs (groovy-ngs-utils API)

Interface Summary
Interface	Description
CompactReadPair.ReadCompressor
Constraint	Represents a constraint in a genetic model
GeneAnnotationSource	Abstract interface for gene annotation sources
IRegion
ReadPair

Class Summary
Class	Description
AcknowledgeableMessage
Align	Utility for helping to perform alignments with BioJava
AltContig
AsciiWriter	Copied from HTSJDK but with constructor modified so that the buffer size can be customized
AsyncMateResolveWorker	A background task that can read from a queue of unpaired reads and resolve their pairs in the background, as well as resolve other reads that are in the same region as the pair that is resolved.
BED	Support for parsing, filtering, and manipuulating BED files.
BED.1
BaseCompactor	A utility to compact bases to a two-per-byte representation
BaseCounts	Stores a set of base counts for a base read at a given position, and supports scoring metrics.
BatchedAcknowledgeableMessage	A batched message automatically accumulates a fixed number of messagse before sending on to a RegulatingActor.
CNVDatabase	Abstract interface that can be implemented by different CNV sources.
CNVFrequency
Cli	This class is a simple utility that configures a CliBuilder how I like it and adds a few simple options that I like.
CliOptions	Wraps a standard OptionAccessor but allows for values to be overridden, enabling classes to be used more generically since OptionAccessor is tied closely to command line.
CompactReadPair	Stores one read of a pair and links to the second read in a way that offers a useful amount of compression for applications that need to store many reads in memory.
CoverageBlock	A run of contiguous bases within a band of coverage depth (eg: a run of low coverage bases).
CoverageGaps	Discovers blocks of low coverage in a file output in BEDTools Coverage format, or alternatively MultiCov output.
CoverageStats	An efficient method to calculate percentiles of coverage values that doesn't require holding them all in memory or sorting them.
DGV	A CNVDatabase implementation for CNVs from the Database of Genomic Variants (sourced via UCSC).
DecipherCNVs	A CNVDatabase implementation for CNVs from Decipher Developmental Delay project.
ExecutedProcess
FASTAIndex	A very simplistic FASTA index that allows lookup of sequence names by their sequence content using a fixed length prefix seed.
FASTHRead	Models a single FASTH read, including the header (with name), barcodes, bases and quality information.
FormatMetaData
GATKIntervalSummary	Reads output of GATK DepthOfCoverage interval summary and makes it available as a Regions object
GATKMeans	Estimates sample means by reading interval summary file output by GATK
GenomeInfo	Static constant information about various genomes used to enable auto-sniffing etc
GenomeResource
GnomADCNVDatabase	A CNVDatabase implementation for CNVs from the gnomAD sv dataset.
GnomADHist
Hash	Simple convenience wrapper that calculates the sha1 hash for a class and returns it formatted in a standard way.
IlluminaFileNameParser
IlluminaSNPData
LiftOver
OMIM	Parser for OMIM genemap files
OrderedPairActor	An actor that adds asynchronous writing to an OrderedPairWriter
OrderedPairReader	A utility class for efficiently iterating all the read pairs in a BAM file.
OrderedPairWriter	When processing reads as pairs it can be tricky to write them out again while maintaining the order expected for a "sorted" BAM file.
OverlapTracker	Simple class to track ranges and remove them when they no longer overlap a given position.
PDF	A light weight PDF Builder for creating PDFs to show results.
Pedigrees
Pileup	Overall class containing pileup state
PileupIterator	Overall class containing pileup state
PileupIterator.Pileup	Inner class that captures pileup state at a specific position
PileupState	Additional state about a read that is part of a pileup
PrefixTrie
ProgressCounter	Simple utility for displaying progress
QualCompactor	A utility to compact quality scores by run length encoding them
RangeIndex	Indexes a set of ranges so that the ranges crossing any point can be identified quickly and easily.
RangeIndex.1
RangeIndex.2
RangeIndex.3
RangeIndex.4
RangedData	RangedData represents a set of genomic regions with data attached.
ReadWindow	Models a window positioned centrally around a location in the genome containing overlapping reads
RefGenes	A convenience class that is set up to parse the UCSC RefGene database as a RangedData object.
RegionIterator
Regions	A set of genomic regions, each indexed by chromosome, start and end position.
RegulatingActor	An Actor that exerts back-pressure to regulate the rate of incoming messages.
RegulatingActor.1
RegulatingActor.2
RepeatMotif
ResolveRequest
SAM	Adds various Groovy idioms and convenience features to the Picard SamReader.
SAMRecordCategory	A convenience class to streamline working with SAMRecord objects
ScannableRegion
SexKaryotyper	An algorithm based on simple heuristics for estimating the sex of a sample from sequencing coverage.
SexKaryotyper.1
SimpleLogFormatter	The default Java log former uses a format that is too verbose, so this class replaces it with something more compact.
SnpEffInfo	Support for parsing annotations from SnpEff
Subject	An individual in a family pedigree
TargetedCNVAnnotator
ToolBase	A support class that makes implementing a tool based on GNGS very easy while supporting some standard behaviors (such as logging, etc).
TwoLeggedOAuthAPI	With 2 legged OAuth there is no need for acquiring an access token or request token; these are presumed known.
VCFIndex	Support for querying indexed VCF files via random access.
VCFIndex.1
VCFSummaryStats	A set of statistics summarizing how a VCF was filtered
VCFWalkPosition	A datastructure to hold thhe state of a given VCF that is being walked
VariantInjector	Injects a variant into a FASTQ read based on recognising the sequence corresponding to the reference sequence for the location of the variant within the read.
XA
XPos	A representation of a genomic position as a long

Enum Summary
Enum	Description
IlluminaFileNameParser.DIALECT
Sex
VepConsequence	Models VEP Consequence type as sourced from https://asia.ensembl.org/info/genome/variation/prediction/predicted_data.html#consequences (Ensembl release 103 - February 2021).

Exception Summary
Exception	Description
Abort	Convenience for aborting loops invoked via closures

Package gngs

Package gngs Description