# All Classes and Interfaces

Class
Description
AcgtTree
ACGT tree
AlleleCountStats
Count singletons and other allele counts per sample
ArrayUtil
Methods for manipulating arrays.
AutoHashMap<K,V>
A Hash that creates new elements if they don't exists
Average
A simple class that calculates averages
AverageInt
A simple class that calculates average of integer numbers
BasesChangeCounter
Counts how many bases changed, given an XOR between two longs
BedAnnotationOutputFormatter
Formats: Show all annotations that intersect the BED input file.
BedFileIterator
Opens a sequence change file and iterates over all intervals in BED format.
BedOutputFormatter
Formats output as BED file Referneces: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
BigBedFileIterator
FileIterator for BigBed features WARNING: Removed in 2022-01 due to dependency on IGV's code (which depends on Log4j, which has a major security issue) Note: I use Broad's IGV code to do all the work, this is just a wrapper
BinarySequence
Base class for a binary 'read'.
Binomial
Calculate binomial distribution References http://en.wikipedia.org/wiki/Binomial_distribution
BinSeqFileIterator<T>
Reads all sequences from a file Warning: You should always call "close()" at the end of the iteration.
BioType
BioTypes: Gene or transcript bioType annotation References: http://www.ensembl.org/info/genome/genebuild/biotypes.html Biotypes classifies genes and transcripts into groups including: protein coding, pseudogene , processed pseudogene, miRNA, rRNA, scRNA, snoRNA, snRNA.
BitUtil
A variety of high efficiency bit twiddling routines.
BlackBoxEvent
A black box event
BlastResultEntry
BlastResultFileIterator
Iterate on each line of a GWAS catalog (TXT format)
BooleanMutable
A mutable boolean
CatalystActivity
A catalyst activity event
Cds
CDS: The coding region of a gene, also known as the coding sequence or CDS (from Coding DNA Sequence), is that portion of a gene's DNA or RNA, composed of exons, that codes for protein.
Chromosome
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
ChromosomeSimpleName
Convert chromosome names to simple names
ChrPosScoreList
A list of invalid input: '<'chromosome, position, scores>
ChrPosStats
How many changes per position do we have in a chromosome.
CircularCorrection
Correct circular genomic coordinates Nomenclature: We use coordinates at the beginning of the chromosme and negative coordinates
CochranArmitageTest
Calculate a Cochran-Armitage test Reference: http://en.wikipedia.org/wiki/Cochran-Armitage_test_for_trend The trend test is applied when the data take the form of a 2 x k contingency table.
Coder
Class used to encode invalid input: '&' decode sequences into binary and vice-versa They are usually stored in 'long' words
CodonChange
Analyze codon changes based on a variant and a Transcript
CodonChangeDel
Calculate codon changes produced by a deletion
CodonChangeDup
Calculate codon changes produced by a duplication
CodonChangeIns
Calculate codon changes produced by an insertion
CodonChangeInterval
Calculate codon changes produced by a Interval Note: An interval does not produce any effect.
CodonChangeInv
Calculate codon changes produced by an inversion
CodonChangeMixed
Calculate codon changes produced by a 'mixed' variant Essentially every 'mixed' variant can be represented as a concatenation of a SNP/MNP + an INS/DEL
CodonChangeMnp
Calculate codon changes produced by a MNP
CodonChangeSnp
Calculate codon changes produced by a SNP
CodonChangeStructural
Calculate codon changes produced by a duplication
CodonTable
A codon translation table
CodonTables
All codon tables are stored here.
CombinatorialIterator
Generate all possible 'count' combinations
CommandLine
Command line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }
CompareByValue
Compare two elements in a Map (e.g.
CompareByValue
Compare two elements in a Map (e.g.
Compartment
A Reactome compartment (a part of a cell)
Complex
A Reactome complex (a bunch of molecules or complexes
Config
CountByKey<T>
Counters indexed by key.
CountByType
Counters indexed by 'type' (type is a generic string that can mean anything)
Counter
A simple class that counts...
CounterDouble
A simple class that counts...
CountFragments
Base by base coverage (one chromsome)
CountReads
Count how many reads map (from many SAM/BAM files) onto markers
CountReadsOnMarkers
Count how many reads map (from many SAM/BAM files) onto markers
Coverage
Base by base coverage (one chromsome)
CoverageByType
CoverageChr
Base by base coverage (one chromsome)
Custom
This is a custom interval (i.e.
CvTerm
A controlled vocabulary term
CytoBands
Cytband definitions E.g.: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz
Depolymerisation
A depolymerization event
Diff
DistanceResult
DnaAndQualitySequence
Binary packed DNA sequence and base calling quality Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 8 bits: - Six bits for the base quality [0 , ..
DnaAndQualitySequenceWithId
DnaAndQualitySequence with an ID
DnaCoder
Class used to encode invalid input: '&' decode sequences into binary and vice-versa Note:This is a singleton class.
DnaNSequence
Binary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}
DnaQualityCoder
Class used to encode invalid input: '&' decode sequences into binary and vice-versa - Every base is encoded in 8 bits: - Six bits for the base quality [0 , ..
DnaQualSubsequenceComparator
Compares two subsequences of DNA (DnaAndQualitySequence)
DnaSeqFileIterator
DnaSeqIdFileIterator
DnaSeqPeFileIterator
DnaSequence
Binary packed DNA sequence Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 2 bits {a, c, g, t} invalid input: '<'=> {0, 1, 2, 3} - All bits are stored in an array of 'words' (integers) - Most significant bits are the first bases in the sequence (makes comparison easier)
DnaSequenceByte
Binary packed DNA sequence.
DnaSequenceId
Binary packed DNA sequence with an ID (long)
DnaSequencePe
Pair end DNA sequence (binary packed) It consists of 2 DNA sequences separated by a gap.
DnaSubsequenceComparator<T>
Compares two subsequences of DNA (DnaSequence)
Download
Command line program: Build database
Downstream
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
EffectType
Effect type: Note that effects are sorted (declared) by impact (highest to lowest putative impact).
EffFormatVersion
VcfFields in SnpEff version 2.X have a different format than 3.X As of version 4.1 we switch to a standard annotation format
Embl
A class representing the same data as an EMBL file References: http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
EmblFile
A file containing one or more set of features (e.g.
EnrichmentAlgorithm
A generic enrichment algorithm for selecting gene-sets from a collection of gene-sets
EnrichmentAlgorithm.EnrichmentAlgorithmType
EnrichmentAlgorithmGreedy
A generic greedy enrichment algorithm for selecting gene-sets
EnrichmentAlgorithmGreedyVariableSize
A greedy enrichment algorithm for selecting gene-sets using a variable geneSet-size strategy: i) Select only from geneSets in low-sizes e.g.
Entity
A reactome basic entity (e.g.
Entity.TransferFunction
ErrorWarningType
Errors and warnings
Event
A reactome event (any generic event, from pathways to polymerizations)
ExecuteOsCommand
Launches an 'OS command' (e.g.
Exon
Interval for an exon
Exon.ExonSpliceType
Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)
ExonSpliceCharacterizer
Characterize exons based on alternative splicing References: "Alternative splicing and evolution - diversification, exon definition and function" (see Box 1)
FastaFileIterator
Opens a fasta file and iterates over all fasta sequences in the file
Fastq2Fastq
Convert FASTQ (phred64) file to FASTQ (phred33)
FastqFileIterator
Opens a fastq file and iterates over all fastq sequences in the file Unlike BioJava's version, this one does NOT load all sequences in memory.
FastqSplit
Split a fastq into N files
FastqTools
Simple maipulation of fastq sequences
FastqTrimmer
Trim fastq sequence when quality drops below a threshold The resulting sequence has to ba at least 'minBases'
FastqTrimmerAdrian
Trim fastq sequence when: - Median quality drops below a threshold (mean is calculated every 2 bases instead of every base) - Sequence length is at least 'minBases' From Adrian Platts ...Also the sliding window was not every base.
FastqTrimmerMedian
Trim fastq sequence when median quality drops below a threshold
Feature
A feature in a GenBank or EMBL file
Feature.Type
FeatureCoordinates
A feature in a GenBank or EMBL file
Features
A class representing a set of features References: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
FeaturesFile
A file containing one or more set of features (e.g.
FileIndexChrPos
Index a file that has "chr \t pos" as the beginning of a line (e.g.
FileIterator<T>
Opens a file and iterates over all objects <T> in the file Note: The file is not loaded in memory, thus allows to iterate over very large files
Filter<T>
A Generic filter interface
FindRareAaIntervals
Find intervals where rare amino acids occur
FisherExactTest
Calculate Fisher's exact test (based on hypergeometric distribution)
FisherPValueAlgorithm
FisherPValueGreedyAlgorithm
FloatStats
A simple class that does some basic statistics on double numbers
FrameType
Type of frame calculations Internally, we use GFF style frame calculation for Exon / Transcript Technically, these are 'frame' and 'phase' which are calculated in different ways UCSC type: Indicated the coding base number modulo 3.
GenBank
A class representing the same data as a GenBank file (a 'GB' file) References: http://www.insdc.org/documents/feature-table http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord
GenBankFile
A file containing one or more set of features (e.g.
Gene
Interval for a gene, as well as transcripts
Gene.GeneType
GeneCountByTypeTable
Count for each 'type' and 'gene'.
GeneIds
Maps different Gene IDs: - ENSEMBL Gene ID to transcript ID - ENSEMBL Gene ID to Gene Name - ENSEMBL Gene ID to Refseq Gene ID - ENSEMBL Gene ID to Refseq Protein ID
GenericMarker
An interval intended as a mark
GenericMarkerFileIterator
Opens a file and creates generic markers (one per line)
Genes
A collection of genes (marker intervals) Note: It is assumed that all genes belong to the same genome
GeneSet
An set of genes (that belongs to a collection of gene-sets)
GeneSets
A collection of GeneSets Genes have associated "experimental values"
GeneSetsRanked
A collection of GeneSets Genes are ranked (usually by 'value')
GeneStats
Some statistics about a gene
Genome
This is just used for the Interval class.
GenomicSequences
This class stores all "relevant" sequences in a genome This class is able to: i) Add all regions of interest ii) Store genomic sequences for those regions of interest iii) Retrieve genomic sequences by interval
Genotypes
Simple test program
GenotypeStats
Calculate statistics on genotype
GenotypeVector
A vector of genotypes in a 'compact' structure Note: Genotypes 0/0, 0/1, 1/0, 1/1 are stored in 2 bits.
Gff3FileIterator
Opens a sequence change file and iterates over all intervals in GFF3 format.
GffMarker
An interval intended as a mark
GffType
GoogleBarChart
GoogleChartVenn
A simple wrapper to goolge charts API (from charts4j) Plots integer data
GoogleGenePercentBar
A simple wrapper to goolge charts API (from charts4j)
GoogleGeneRegionChart
GoogleGeneRegionNumExonsChart
GoogleHistogram
A simple wrapper to goolge charts API (from charts4j)
GoogleLineChart
GooglePlot
A simple wrapper to goolge charts API (from charts4j)
GooglePlotInt
A simple wrapper to goolge charts API (from charts4j) Plots integer data
GoTerm
An instance of a GO term (a node in the DAG)
GoTerms
A collection of GO terms
Gpr
General pupose rutines
GprHtml
General stuff realted to HTML
GprSeq
Gtex
Load data from GTEx files.
GtexExperiment
A 'column' in a GTEx file (values from one experiment
Gtf2Marker
An interval intended as a mark
GuessTableTypes
Given a table in a TXT file, try to guess the value types for each column
HashLongLongArray
A Hashinvalid input: '<'long, long[]> using primitive types instead or warped object The idea is to be able to add many long values for each key This could be implemented by simply doing HashMapinvalid input: '<'Long, Set<Long> > (but it would consume much more memory) Note: We call each 'long[]' a bucket WARNING: This collection does NOT allow elements to be deleted! But you can replace values.
Hgvs
HGSV notation References: http://www.hgvs.org/
HgvsDna
Coding DNA reference sequence References http://www.hgvs.org/mutnomen/recs.html Nucleotide numbering: - there is no nucleotide 0 - nucleotide 1 is the A of the ATG-translation initiation codon - the nucleotide 5' of the ATG-translation initiation codon is -1, the previous -2, etc.
HgvsProtein
Coding change in HGVS notation (amino acid changes) References: http://www.hgvs.org/mutnomen/recs.html
HomHetStats
Count Hom/Het per sample From Pierre: For multiple ALT, I suggest to count the number of REF allele 0/1 => ALT1 0/2 => ALT1 1/1 => ALT2 2/2 => ALT2 1/2 => ALT2
Hypergeometric
Calculate hypergeometric distribution using an optimized algorithm that avoids problems with big factorials.
IdGenerator
Generates Id
IdMap
Maps many IDs to many Names I.e.
IdMapper
Map protein ID to transcript ID and vice versa
IdMapperEntry
An entry in a ID mapping file
Intergenic
Interval for in intergenic region
IntergenicConserved
Interval for a conserved intergenic region
Interval
A genomic interval.
IntervalAndSubIntervals<T>
Interval that contains sub intervals.
IntervalComparatorByEnd
Compare intervals by end position
IntervalComparatorByStart
Compare intervals by start position
IntervalForest
A set of interval trees (e.g.
IntervalNode
Node for interval tree structure
IntervalNodeOri
The Node class contains the interval tree information for one single node
IntervalSetIterator
Iterate over intervals.
IntervalTree
An Interval Tree is essentially a map from intervals to objects, which can be queried for all data associated with a particular interval of point
IntervalTreeArray
Interval tree structure using arrays This is slightly faster than the new IntervalTree implementation
IntervalTreeOri
An Interval Tree is essentially a map from intervals to objects, which can be queried for all data associated with a particular interval of point
IntHisto
Histogram of integer numbers
Intron
Intron
IntronConserved
Interval for a conserved non-coding region in an intron
IntStats
A simple class that does some basic statistics on integer numbers
Iterator2Iterable<T>
Convert an iterator instance to a (fake) iterable
Itree
Interval tree interface
IubString
Find all bases combinations from a string containing IUB codes
Jaspar
Load PWM matrices from a Jaspar file
KeyValue<A,B>
A "key = value" pair
LeadingEdgeFractionAlgorithm
Leading edge fraction algorithm References: "Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits" http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001058 See page 12, "Step 4"
LineChrPos
A simple chr:pos parser Stores using bytes instead of chars
LineClassFileIterator<T>
Iterate on each line.
LineFileIterator
Iterate on each line in this file
LineFilter
Filter a line before processing
LineSeqFileIterator
One line per sequence.
Location
A location (i.e.
LocationTargetIsoform
A location respect to an isoform
LocationTargetIsoformInteraction
A location respect to two locations within an isoform In this case "start" and "end" are not really an interval, but an interaction between two locations (e.g.
Log
Logging
Log.FatalErrorBehabiour
LogStats
Log basic usage information to a server (for feedback and stats) This information an always be suppressed (no info sent at all)
LogStats.RequestResult
LossOfFunction
Analyze if a set of effects are can create a "Loss Of Function" and "Nonsense mediated decays" effects.
Marker
An interval intended as a mark (i.e.
MarkerFileIterator<M>
Opens a Marker file and iterates over all markers
MarkerParentId
This is a marker used as a 'fake' parent during data serialization
Markers
A collection of markers
MarkerSeq
Marker with a DNA sequence
MarkerSerializer
Serialize markers to (and from) file
MarkerTypes
Create a list of marker types (names or labels for markers)
MarkerUtil
Generic utility methods for Markers
MarkerWithFrame
A Marker that has 'frame' information (Exon and Cds)
MatrixEntry
A simple entry in a 'Matrix' file
MatrixEntryFileIterator
Iterate on each line of a file, creating a MatrixEntry
MicroCosmEntry
Entry in a MicroCosm (miRNA target prediction) file
MicroCosmFileIterator
Iterate on each line of a MicroCosm predictions References: http://www.ebi.ac.uk/enright-srv/microcosm/
MicroRnaBindingSite
miRna binding site (usually this was predicted by some algorithm)
MineMarkerIntervals
Mine marker intervals: I.e.
MineTwoMarkerIntervals
Mine marker intervals: I.e.
Monitor
Motif
Regulatory elements
MotifFileIterator
Opens a regulation file and create Motif elements.
MotifLogo
Create a DNA logo for a PWM References: - See WebLogo http://weblogo.berkeley.edu/ - "WebLogo: A Sequence Logo Generator"
MultivalueHashMap<K,V>
A Hash that can hold multiple values for each key
NeedlemanWunsch
Needleman-Wunsch (global sequence alignment) algorithm for sequence alignment (short strings, since it's not memory optimized)
NeedlemanWunschOverlap
Needleman-Wunsch algorithm for string alignment (short strings, since it's not memory optimized)
NextProt
NextProt annotation marker
NextProtDb
Parse NetxProt XML file and build a database
NextProtHandler
Handler used in XML parsing for NextProt database It keeps track of the tags and saves state data to create Markers using NextProtMarkerFactory http://www.nextprot.org/
NextProtMarkerFactory
Creates Markers from nextprot XML annotations
NextProtSequenceConservation
A simple analysis of sequence conservation for each entry type Why? Many NextProt annotations are only a few amino acids long (or only 1 AA) and often they only involve very specific sequences If the sequence is highly conserved and a non-synonymous mutation occurs, then this might be disruptive (i.e.
NextProtXmlAnnotation
Mimics the 'annotation' tag in a NextProt XML file
NextProtXmlEntry
Mimics the 'entry' in a NextProt XML file
NextProtXmlIsoform
Mimics the 'isoform-mapping' in a NextProt XML file
NextProtXmlNode
Mimics a node in NextProt XML file
Nmer
Binary packed N-mer (i.e.
NmerCount
Mark if an Nmer has been 'seen' It only count up to 255 (one byte per counter)
NmerCountWc
Create a counter that can count Nmers as well as their WC complements That means that given an Nmer, the nmer and the Watson-Crick complement are counted the same.
NoneAlgorithm
An algorithm that does nothing
NormalDistribution
Calculate Normal distribution (PDF invalid input: '&' CDF) using more precision if required
NullReader
A buffered reader for a file.
ObservedOverExpected
Observed over expected values (o/e) ratios E.g.: CpG dinucleotides in a sequence
ObservedOverExpectedCHG
Observed over expected values (o/e) of CHG in a sequence
ObservedOverExpectedCHH
Observed over expected values (o/e) of CHH in a sequence
ObservedOverExpectedCpG
Observed over expected values (o/e) of CpG in a sequence
OpenBitSet
An "open" BitSet implementation that allows direct access to the array of words storing the bits.
OsCmdQueue
A queue of commands to be run.
OsCmdRunner
Run an OS command as a thread
OutputFormatter
Formats output How is this used: - newSection(); // Create a new 'section' on the output format (e.g.
Overlap<S>
Calculates the best overlap between two sequences Note: An overlap is a simple 'alignment' which can only contain gaps at the beginning or at the end of the sequences.
OverlapDnaSeq
OverlapFilter<T>
Indicate whether an overlap between two sequences should be considered or not
OverlapFilterCompareAllAll
Only allow overlaps between sequences mapped to same/different partition
OverlapFilterDnaId
Only allow sequences with different IDs to be overlapped
OverlapRessult<T>
An object used to store overlap parameters
Parser<T>
Parse a string and return a collection of objects.
Pathway
A Reactome pathway
Pcingola
Author's data
PdbFile
A structure that reads PDB files
PdbUtil
PedEntry
An entry in a PED table.
PedFamily
A family: A group of Tfams with the same familyId
PedFileIterator
PED file iterator (PED file from PLINK) Reference: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
PedGenotype
A Simple genotype implementation for PED files
Pedigree
A pedigree for cancer samples
PedigreeEntry
Pedigree entry in a VCF file header E.g.: ##PEDIGREE=invalid input: '<'Derived=Patient_01_Somatic,Original=Patient_01_Germline> or ##PEDIGREE=invalid input: '<'Child=CHILD-GENOME-ID,Mother=MOTHER-GENOME-ID,Father=FATHER-GENOME-ID>
PedPedigree
A pedigree of PedEntries
PlinkMap
PLINK MAP file References: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
Polymerisation
A polymerization event
PosStats
How many changes per position do we have in a chromosome.
Progress
PromoterSequences
Get promoter sequences from genes
ProteinFastaWriter
Writes protein sequences to a FASTA file
ProteinInteractionLocus
Protein interaction: An amino acid that is "in contact" with another amino acid.
ProteinInteractions
This class reads a set of protein structure (PDB) files, analyzes the structures, and creates a interactions file for a SnpEff genome database (interactions.bin)
ProteinProteinInteractionLocus
Protein interaction: An amino acid that is "in contact" with another amino acid within the same protein.
ProteinStructuralInteractionLocus
Protein interaction: An amino acid that is "in contact" with another amino acid.
PurityChange
Analize purity changes in codons and amino acids
PvaluesList
A list of pvalues (i.e.
Pwm
Create a DNA motif count matrix Refrence http://en.wikipedia.org/wiki/Position-specific_scoring_matrix
PwmAndSeqs
Create a DNA motif count matrix and also count the number of sequences in that contribute to this motif.
Qseq2Fastq
Convert qseq file to fastq
RandMarker
Create random markers using a uniform distribution
RankSumNoReplacementPdf
Calculate rank sum probability distribution function (pdf) and cumulative distribution function (cdf).
RankSumNoReplacementSimulate
Calculate rank sum probability distribution function (pdf) and cumulative distribution function (cdf).
RankSumPdf
Calculate rank sum probability distribution function (pdf) and cumulative distribution function (cdf).
RankSumPValueAlgorithm
RankSumPValueGreedyAlgorithm
RareAminoAcid
Rare amino acid annotation: These are amino acids that occurs very rarely in an organism.
Reaction
A reaction
Reaction.RegulationType
Reaction regulation types
Reactome
Load reactome data from TXT files
ReadsOnMarkersModel
Calculate the maximum interval length by type, for all markers in a genome Create a probability model based on binomial ditribution.
Regulation
Regulatory elements
RegulationBedFileIterator
Opens a GFF3 file and create regulatory elements.
RegulationConsensusMultipleBed
Create a regulation consensus from multiple BED files
RegulationFileConsensus
Create a regulation consensus from a regulation file.
RegulationFileIterator
Opens a regulation file and create Regulation elements.
RegulationFileSplitBytType
Split regulation files into smaller files (one per 'regulation type') Regulation files can be quite large and we cannot read them into memory.
RegulationGffFileIterator
Opens a GFF3 file and create regulatory elements.
ReSampleInt
Re-sample statistic Statistic is a sum of a set of integer numbers (e.g.
ReSampleMap
Resample statistic
ReSampleMapRank
Re-sample statistic using ranks of scores (scores are double)
Result
Store a result form a greedy search algorithm
SamEntry
An entry in a SAM file References: http://samtools.sourceforge.net/SAM-1.3.pdf
SamFileIterator
Reads a SAM file Note: This is a very 'rustic' reader (we should use Picard's API instead)
SamHeader
Sam header
SamHeaderRecord
Sam header record
SamHeaderRecordSq
SQ header: Reference sequence dictionary.
SamplingStats<T>
Perform stats by analyzing some samples
ScoreList
A list of scores
ScoreList.ScoreSummary
SeekableBufferedReader
A buffered reader for a file.
SequenceComplexity
Measures the complexity of a sequence Ideally we'd like to measure the Kolmogorov complexity of the sequence.
SequenceIndexer<T>
A collection of sequences that are indexed using some algorithm Note: The ID is just the position in the array.
SequenceReference
A reference to a sequence.
SequenceRotator
Rotates a binary packed sequence WARNING: We only rotate up to Coder.basesPerWord() because after that the sequences are the same (with an integer offset) NOTE: Left rotation 'n' is the same as a right rotation 'Coder.basesPerWord() - n'
Sex
SmithWaterman
Smith-Waterman (local sequence alignment) algorithm for sequence alignment (short strings, since it's not memory optimized)
SnpEff
SnpEff's main command line program
SnpEff.GeneDatabaseFormat
Available gene database formats
SnpEff.InputFormat
Available input formats
SnpEff.OutputFormat
Available output formats
SnpEffCmdAcat
ACAT: Create ACAT score for T2D project Note: This is just used to compile 'ACAT' score in T2D-GENES project, not useful at all for general audience.
SnpEffCmdBuild
Command line program: Build database
SnpEffCmdBuildNextProt
Parse NetxProt XML file and build a database http://www.nextprot.org/
SnpEffCmdCds
Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structures
SnpEffCmdClosest
Command line: Find closes marker to each variant
SnpEffCmdCount
Count reads from a BAM file given a list of intervals
SnpEffCmdDatabases
Show all databases configures in snpEff.config Create an HTML 'download' table based on the config file Also creates a list of genome for Galaxy menu
SnpEffCmdDownload
Command line program: Download and install a (pre built) database
SnpEffCmdDump
Command line program: Build database
SnpEffCmdDump.DumpFormat
SnpEffCmdEff
Command line program: Predict variant effects
SnpEffCmdGenes2Bed
Simple test program
SnpEffCmdGsa
Command line: Gene-Sets Analysis Perform gene set analysys
SnpEffCmdLen
Calculate the maximum interval length by type, for all markers in a genome
SnpEffCmdPdb
PDB distance analysis
SnpEffCmdProtein
Command line: Read protein sequences from a file and compare them to the ones calculated from our data structures Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.
SnpEffCmdSeq
Command line program: Show a transcript or a gene
SnpEffCmdShow
Command line program: Show a transcript or a gene
SnpEffCmdSpliceAnalysis
Analyze sequences from splice sites
SnpEffCmdTranslocationsReport
Create an SVG representation of a Marker
SnpEffectPredictor
Predicts effects of SNPs
SnpEffPredictorFactory
This class creates a SnpEffectPredictor from a file (or a set of files) and a configuration
SnpEffPredictorFactoryEmbl
This class creates a SnpEffectPredictor from an Embl file.
SnpEffPredictorFactoryFeatures
This class creates a SnpEffectPredictor from a 'features' file.
SnpEffPredictorFactoryGenBank
This class creates a SnpEffectPredictor from a GenBank file.
SnpEffPredictorFactoryGenesFile
This class creates a SnpEffectPredictor from a file (or a set of files) and a configuration The files used are: - genes.txt : Biomart query from Ensembl (see scripts/genes_dataset.xml) - Fasta files: One per chromosome (as described in the config file)
SnpEffPredictorFactoryGff
This class creates a SnpEffectPredictor from a GFF file.
SnpEffPredictorFactoryGff2
This class creates a SnpEffectPredictor from a GFF2 file.
SnpEffPredictorFactoryGff3
This class creates a SnpEffectPredictor from a GFF3 file References: - http://www.sequenceontology.org/gff3.shtml - http://gmod.org/wiki/GFF3 - http://www.eu-sol.net/science/bioinformatics/standards-documents/gff3-format-description
SnpEffPredictorFactoryGtf22
This class creates a SnpEffectPredictor from a GTF 2.2 file References: http://mblab.wustl.edu/GTF22.html
SnpEffPredictorFactoryKnownGene
This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser Fields in this table Field Example SQL type Info Description ----- ------- -------- ---- ----------- name uc001aaa.3 varchar(255) values Name of gene chrom chr1 varchar(255) values Reference sequence chromosome or scaffold strand + char(1) values + or - for strand txStart 11873 int(10) unsigned range Transcription start position txEnd 14409 int(10) unsigned range Transcription end position cdsStart 11873 int(10) unsigned range Coding region start cdsEnd 11873 int(10) unsigned range Coding region end exonCount 3 int(10) unsigned range Number of exons exonStarts 11873,12612,13220, longblob Exon start positions exonEnds 12227,12721,14409, longblob Exon end positions proteinID varchar(40) values UniProt display ID for Known Genes, UniProt accession or RefSeq protein ID for UCSC Genes alignID uc001aaa.3 varchar(255) values Unique identifier for each (known gene, alignment position) pair
SnpEffPredictorFactoryRand
This class creates a random set of chromosomes, genes, transcripts and exons
SnpEffPredictorFactoryRefSeq
This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser RefSeq table schema: http://genome.ucsc.edu/cgi-bin/hgTables field example SQL type info description bin 585 smallint(5) range Indexing field to speed chromosome range queries.
SpliceSite
Interval for a splice site Reference: http://en.wikipedia.org/wiki/RNA_splicing Spliceosomal introns often reside in eukaryotic protein-coding genes.
SpliceSiteAcceptor
Interval for a splice site acceptor Note: Splice sites donnor are defined as the last 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicing
SpliceSiteBranch
A (putative) branch site.
SpliceSiteBranchU12
A (putative) U12 branch site.
SpliceSiteDonor
Interval for a splice site donnor Note: Splice sites donnor are defined as the first 2 bases of an intron Reference: http://en.wikipedia.org/wiki/RNA_splicing
SpliceSiteRegion
Interval for a splice site acceptor From Sequence Ontology: A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
SpliceTypes
Analyze sequences from splice sites
StreamGobbler
Read the contents of a stream in a separate thread This class is used when executing OS commands in order to read STDOUT / STDERR and prevent process blocking It can alert an AlertListener when a given string is in the stream
StringDiff
SubsequenceComparator<T>
Compare two subsequences (actually it compares two sequences from different starting points)
SuffixIndexerNmer<T>
Index all suffixes of all the sequences (it indexes using Nmers).
Svg
Create an SVG representation of a Marker
SvgBnd
Create an SVG representation of a BND (translocation) variant In a VCF file, there are four possible translocations (BND) entries: REF ALT Meaning type 1: s t[p[ piece extending to the right of p is joined after t type 2: s t]p] reverse comp piece extending left of p is joined after t type 3: s ]p]t piece extending to the left of p is joined before t type 4: s [p[t reverse comp piece extending right of p is joined before t
SvgCds
Create an SVG representation of a Marker
SvgExon
Create an SVG representation of a Marker
SvgGene
Create an SVG representation of a Marker
SvgIntron
Create an SVG representation of a Marker
SvgNextProt
Create an SVG representation of a NextProt annotation tracks
SvgScale
Create an SVG representation of a "Scale and Chromsome labels
SvgSpacer
Leave an empty vertical space
SvgTranscript
Create an SVG representation of a transcript
SvgTranslocation
Create an SVG representation of a BND (translocation) variant In a VCF file, there are four possible translocations (BND) entries: REF ALT Meaning type 1: s t[p[ piece extending to the right of p is joined after t type 2: s t]p] reverse comp piece extending left of p is joined after t type 3: s ]p]t piece extending to the left of p is joined before t type 4: s [p[t reverse comp piece extending right of p is joined before t
TableFile
Load a table from a file.
TfamEntry
An entry in a TFAM table.
Timer
Transcript
Interval for a transcript, as well as some other information: exons, utrs, cds, etc.
TranscriptSet
A set of transcripts
TranscriptSupportLevel
Transcript level support Reference: http://useast.ensembl.org/Help/Glossary?id=492;redirect=no
TranslocationReport
Pojo for translocation reports
TsTvStats
Calculate Ts/Tv rations per sample (transitions vs transversions)
Tuple<A,B>
Tuple: A pair of objects
TxtSerializable
Upstream
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
Utr
Interval for a UTR (5 prime UTR and 3 prime UTR
Utr3prime
Interval for a UTR (5 prime UTR and 3 prime UTR
Utr5prime
Interval for a UTR (5 prime UTR and 3 prime UTR
Variant
A variant represents a change in a reference sequence As of version 4.0, variants have no strand, i.e.
Variant.VariantType
VariantBnd
A 'BND' variant (i.e.
VariantEffect
Effect of a variant.
VariantEffect.Coding
VariantEffect.EffectImpact
VariantEffect.FunctionalClass
This class is only getFused for SNPs
VariantEffectFilter
A Generic ChangeEffect filter
VariantEffectFusion
Effect of a structural variant (fusion) affecting two genes
VariantEffects
A sorted collection of variant effects
VariantEffectStats
Variants annotation statistics.
VariantEffectStructural
Effect of a structural variant affecting multiple genes
VariantFileIterator
Opens a sequence change file and iterates over all sequence changes
VariantNonRef
A variant respect to non-reference (e.g.
VariantRealign
Re-align a variant towards the leftmost (rightmost) position Note: We perform a 'progressive' realignment, asking for more reference sequence as we need it
VariantStats
Variants statistics: These are statisticas at Variant level.
VariantTxtFileIterator
Opens a sequence change file and iterates over all sequence changes TXT Format: Tab-separated format, containing five columns that correspond to: chr \t position \t refSeq \t newSeq \t strand \t quality \t coverage \t id \n Fields strand, quality, coverage and id are optional E.g.
VariantTypeStats
Count variant types (SNP, MNP, INS, DEL)
VariantVcfEntry
Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.
VariantWithScore
A variant that has a numeric score.
VcfAnnotator
Annotate a VCF file: E.g.
VcfAnnotatorChain
Maintains a list of VcfAnnotators and applies them one by one in the specified order
VcfConsequence
An 'CSQ' entry in a vcf line ('Consequence' from ENSEMBL's VEP) Format: ##INFO=invalid input: '<'ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP.
VcfConsequenceHeader
An 'CSQ' entry in a vcf header line
VcfEffect
An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *
VcfEntry
A VCF entry is a line in a VCF file A VCF line can have multiple variants, and multiple genotypes The VcfEntry represents the VCF line, NOT the variant itself.
VcfEntry.AlleleFrequencyType
VcfFileIterator
Opens a VCF file and iterates over all entries (i.e.
VcfGenotype
A VCF genotype field There is one genotype per sample in each VCF entry
VcfHapMapFileIterator
Opens a Hapmap phased file and iterates over all entries, returning VcfEntries for each line Note: Each HapMap file has one chromosome.
VcfHeader
Represents the header of a vcf file.
VcfHeaderEntry
Represents a info elements in a VCF file's header References: https://samtools.github.io/hts-specs/VCFv4.3.pdf http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
VcfHeaderFormat
VcfHeaderInfo
Represents a info elements in a VCF file References: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 INFO fields should be described as follows (all keys are required): ##INFO=invalid input: '<'ID=ID,Number=number,Type=type,Description=description> Possible Types for INFO fields are: Integer, Float, Flag, Character, and String.
VcfHeaderInfo.VcfInfoNumber
Number of values in an INFO field.
VcfInfoType
VcfLof
An 'LOF' entry in a vcf line
VcfNmd
An 'NMD' entry in a vcf line
VcfOutputFormatter
Formats output as VCF
VcfRefAltAlign
Needleman-Wunsch (global sequence alignment) algorithm for sequence alignment Only used for short strings (algorithm is not optimized)
VcfStats
VCF statistics: These are statisticas at VCF line (i.e.
VersionCheck
Check is a new version is available
Zzz
How to calculate hydrogen bonds: - https://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(or%20H,hydrogen%20bond%20acceptor%20(Ac).