- A - Field in BaseCompactor
-
- a - Property in BaseCounts
-
- Abort - Class in gngs
Convenience for aborting loops invoked via closures
- Abort(java.lang.String, java.lang.Throwable) - Constructor in Abort
-
- abort() - Method in BED.1
-
- AcknowledgeableMessage - Class in gngs
- AcknowledgeableMessage(T, java.util.concurrent.atomic.AtomicInteger) - Constructor in AcknowledgeableMessage
-
- acknowledgeCounter - Field in AcknowledgeableMessage
-
- act() - Method in OrderedPairActor
-
- act() - Method in RegulatingActor
-
- activeRanges - Property in RangeIndex.2
-
- activeRanges - Property in RangeIndex.3
-
- actor(groovy.lang.Closure) - Method in RegulatingActor
-
- actors - Property in PairScanner
-
- add(java.lang.String, int, int, java.lang.Object) - Method in BED
-
Add the specified range to this BED file.
- add(int[]) - Method in OverlapTracker
-
- add(gngs.Pedigree) - Method in Pedigrees
-
Add the pedigree to this Pedigrees object
- add(java.lang.String, T, int) - Method in PrefixTrie
-
- add(groovy.lang.IntRange) - Method in RangeIndex
-
- add(java.lang.String, T) - Method in TrieNode
-
- add(java.lang.String, gngs.Pedigrees, gngs.Variant, gngs.Variant$Allele, java.lang.String, java.lang.String, java.lang.Object) - Method in VariantDB
-
Add the given variant to the database.
- addAlignmentPair(gngs.SAMRecordPair) - Method in OrderedPairActor
-
- addAlignmentPair(gngs.SAMRecordPair) - Method in OrderedPairWriter
-
- addCachedSampleInfo(List<String>, java.lang.String, java.lang.String, gngs.Pedigrees) - Method in VariantDB
-
Returns cached rows from the sample table for each sample.
- addChild(gngs.gencode.Feature) - Method in Feature
-
- addContainedEntry(Map.Entry<Integer, List<IntRange>>, Map.Entry<Integer, List<IntRange>>, groovy.lang.IntRange) - Method in RangeIndex
-
Add a reference to a range to a breakpoint that falls in the middle of the range
- addPosition - Property in PairFormatter
-
If true, the original position of the read will be appended
to the read name.
- addPosition - Property in PairScanner
-
- addPositionToNames - Property in ExtractFASTQ
-
- addPreprocessedRead(gngs.SAMRecordPair) - Method in OrderedPairReader
-
- addRegion(gngs.Region) - Method in Regions
-
Adds the region to this Regions object in such a way that the same Region
object is returned in iteration, preserving any expando properties set on
the region.
- addSample(java.lang.String, gngs.Pedigrees, java.lang.String, java.lang.String) - Method in VariantDB
-
Add information about the given sample to the database
- addSampleBatch(java.lang.Long, java.lang.String, java.lang.String) - Method in VariantDB
-
- AFRICAN - Field in Ethnicity
-
- Align - Class in gngs
Utility for helping to perform alignments with BioJava
- Align() - Constructor in Align
-
- align(java.lang.String, groovy.lang.Closure) - Method in PDF
-
Set alignment within table cells
- ALIGNMENT_DEFAULTS - Property in Align
-
- alignmentEnd - Field in ReadRange
-
- alignments - Field in Pileup
-
- alignments - Field in PileupIterator
-
- alignmentStart - Field in ReadRange
-
- allele1 - Property in IlluminaSNPData
-
Call of first allele relative to forward strand
- allele2 - Property in IlluminaSNPData
-
Call of first second allele relative to forward strand
- alleleFraction - Property in VariantInjector
-
- AlleleNumber - Class in gngs.tools
A utility class to contain some functionality for computing allele numbers / counts
- AlleleNumber() - Constructor in AlleleNumber
-
- allRanges - Property in Regions
-
A list of ranges in the order they were loaded
- allStats - Property in BEDToolsCoverage
-
- AltContig - Class in gngs
- AltContig(java.lang.String, java.lang.String, int, java.lang.String) - Constructor in AltContig
-
- altIds - Property in SampleInfo
-
Recognised alternative identifiers for the sample
- AMELY_BASES - Property in Sex
-
- analyseChromosome(java.lang.String) - Method in Delfin
-
- analysisContact - Property in SampleInfo
-
- annotate(gngs.IRegion, java.lang.String) - Method in TargetedCNVAnnotator
-
Compute the frequency of CNVs in databases that are compatible with a CNV
identified in the given range, and matching the given type
- annotateFromDatabase(gngs.CNVDatabase, gngs.IRegion, java.lang.String) - Method in TargetedCNVAnnotator
-
- annotateGapRegion(gngs.Region) - Method in GapAnnotator
-
- annotateGenes(List<Map>) - Method in Table
-
- annotateSize(gngs.IRegion) - Method in TargetedCNVAnnotator
-
- ANNOTATION_COLUMNS - Property in GapAnnotator
-
Names of properties set as annotations on gap regions
- ANNOTATION_OUTPUT_COLUMNS - Property in GapAnnotator
-
Prettier human readable version of above columns - should always match 1-1
- annotationProfile - Property in VariantDB
-
- annotations - Property in CoverageBlock
-
- ANNOVAR_ANNOTATION_PROFILE - Property in VariantDB
-
- appendTo(java.lang.String, java.lang.StringBuilder, java.lang.StringBuilder, gngs.pair.Paired, boolean) - Method in CompactReadPair
-
- applyCellProperties(com.lowagie.text.pdf.PdfPCell) - Method in PDF
-
- arguments() - Method in CliOptions
-
- AsciiWriter - Class in gngs
Copied from HTSJDK but with constructor modified so that the buffer size can be customized
- AsciiWriter(java.io.OutputStream, int) - Constructor in AsciiWriter
-
- Parameters:
os - need not be buffered as this class buffers
- ASIAN - Field in Ethnicity
-
- asType(java.lang.Class) - Method in CoverageBlock
-
- asType(java.lang.Class) - Method in CoverageGaps
-
- asType(java.lang.Class) - Method in SAM
-
- asType(htsjdk.samtools.BAMRecord, java.lang.Class) - Method in SAMRecordCategory
-
- AsyncMateResolveWorker - Class in gngs
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.
- AsyncMateResolveWorker() - Constructor in AsyncMateResolveWorker
-
- asyncRequests - Property in OrderedPairReader
-
- asyncResolves - Property in OrderedPairReader
-
- AUTO_COLUMN_NAMES - Property in Table
-
- autosomeChrs - Property in SexKaryotyper
-
- autosomeCoverage - Property in SexKaryotyper
-
- background(java.lang.String, groovy.lang.Closure) - Method in PDF
-
Set background color of table cells
- backward(java.lang.String, int, int) - Method in Regions
-
Returns the region that is count regions backwards from the given position
- balancedSplit() - Method in Regions
-
Divide these regions into two regions objects with approximately the same
total bp in each half
- bam - Property in DeletionPlot
-
- bam - Property in ExtractFASTQ
-
- bam - Property in MeanCoverageEstimator
-
- bam - Property in OrderedPairReader
-
- bam - Property in Pairs
-
- bam - Property in PairScanner
-
- bam - Property in SexKaryotyper
-
- bam - Property in TargetedCoverageCalculator
-
- bams - Property in GeneCovStats
-
- bams - Property in MultiCov
-
- banner(java.lang.String) - Method in Cli
-
- bar(gngs.IRegion, java.lang.Object, java.lang.String, java.lang.String) - Method in Drawing
-
- barcodebases - Property in FASTHRead
-
- barcodequals - Property in FASTHRead
-
- base - Field in PileupState
-
- BaseCompactor - Class in gngs
A utility to compact bases to a two-per-byte representation
- baseCompressionStats - Field in CompactReadPair
-
- BaseCounts - Class in gngs
Stores a set of base counts for a base read at a given position,
and supports scoring metrics.
- BaseCounts(List<String>, int) - Constructor in BaseCounts
-
- baseMean - Property in CoverageSummary
-
- baseQualityTag - Property in PairScanner
-
The tag from which to extract base quality scores (use actual base qualities if null)
- basesAt(java.lang.String, int) - Method in SAM
-
Return a Map with a key for each base observed at the given position,
with the value being the number of times that base was observed.
- batch - Property in SampleInfo
-
Id of batch in which the sample was sequenced
- BatchedAcknowledgeableMessage - Class in gngs
A batched message automatically accumulates a fixed number of messagse before sending
on to a
RegulatingActor.
- BatchedAcknowledgeableMessage(BatchedAcknowledgeableMessage<T>) - Constructor in BatchedAcknowledgeableMessage
-
- batchTo(T, RegulatingActor<T>) - Method in BatchedAcknowledgeableMessage
-
- BED - Class in gngs
Support for parsing, filtering, and manipuulating BED files.
- BED.1 - Class in gngs
- BED.1() - Constructor in BED.1
-
- BED(java.util.Map, Iterable<Region>) - Constructor in BED
-
Create a BED from a list of regions
- bedFile - Property in BED
-
File from which bed is read
- bedFileStream - Property in BED
-
The stream from which bed line will be read
- BEDToolsCoverage - Class in BEDToolsCoverage
- BEDToolsCoverage(java.lang.String, gngs.Regions) - Constructor in BEDToolsCoverage
-
- bestScore() - Method in BaseCounts
-
- bg(java.lang.String, groovy.lang.Closure) - Method in PDF
-
- bins - Property in GnomADHist
-
- bkr() - Method in Regions
-
- block - Property in CoverageGaps
-
- blockCount - Property in CoverageGaps
-
- blocks - Property in CoverageGaps
-
Discovered gaps (the results) are stored here for access after calling
calculate
- bold(groovy.lang.Closure) - Method in PDF
-
- br(int) - Method in PDF
-
- buffer2 - Property in PairFormatter
-
- buffer - Property in OrderedPairWriter
-
- buffer - Property in PairFormatter
-
- BUFFER_SIZE_BYTES - Property in CoverageGaps
-
Use a large buffer for very efficient reading
- BUFFER_SIZE - Field in VCFIndex
-
A 256 kb memory buffer that will try to minimize operations
on the indexed file
- buffered - Property in PairFormatter
-
- C - Field in BaseCompactor
-
- c - Property in BaseCounts
-
- cachedSampleInfo - Property in VariantDB
-
Map of string to database rows of cached sample information
- calcCovStats(gngs.Regions) - Method in SexKaryotyper
-
- calcGeneStats(gngs.Regions) - Method in GeneCovStats
-
- calculate() - Method in CoverageGaps
-
- calculateChrCoverage(java.lang.String, int[], int) - Method in TargetedCoverageCalculator
-
Count the number of reads overlapping each target region from the given chromosome
- calculateFromBEDTools(java.io.Reader) - Method in CoverageGaps
-
- calculateFromMultiCov(java.io.Reader) - Method in CoverageGaps
-
- calculateGeneMasterStats(gngs.Regions) - Method in GeneCovStats
-
- calculateIntervalGCs() - Method in Delfin
-
- calculateMeans(List<String>) - Method in GATKMeans
-
- calculateMultiCov() - Method in CoverageGaps
-
- callAndOptimise(java.lang.String, java.lang.String, graxxia.Matrix, graxxia.Matrix, graxxia.Matrix) - Method in Delfin
-
Tries calling deletions while removing increasing numbers of prinicipal components.
- captureDates - Property in SampleInfo
-
- cell(java.lang.Object) - Method in PDF
-
- cells(java.lang.Object) - Method in PDF
-
- chainFile - Property in LiftOver
-
- check(java.lang.Object, java.util.List) - Method in Cli
-
- checkRanges(int) - Method in RangeIndex
-
Check that all the ranges added at a position span that position
- checkSchema(groovy.sql.Sql) - Method in Schema
-
Iterate over the schema versions and check if they exist
- children - Property in Feature
-
- children - Property in TrieNode
-
- chimeric - Property in PairScanner
-
- chimericPreprocessedReads - Property in OrderedPairReader
-
To contain memory consumption, preprocessed reads are cleared every chromosome.
- chr - Property in CoverageBlock
-
- chr - Property in CoveragePosition
-
- chr - Property in Feature
-
- chr - Property in IlluminaSNPData
-
- chr - Field in Pileup
-
- chr - Field in PileupIterator
-
- chr - Property in PositionCounts
-
- chr - Property in SampleReadCount
-
- chr - Property in XA
-
- chrColumn - Property in BED
-
Columns for reading the position data - these can be overridden to allow
loading of any "bed-like" file
- chrColumn - Property in RangedData
-
Index of the column containing the reference sequence (or "chromosome")
- chromosomesWithReads - Property in PairScanner
-
- chrToInt(java.lang.String) - Method in XPos
-
- cigar - Field in PileupState
-
- cigar - Property in XA
-
- cigarElement - Field in PileupState
-
- cigarIterator - Field in PileupState
-
- cigarPos - Field in PileupState
-
Offset within the current cigar element
- cigarString - Property in AltContig
-
- clear() - Method in OverlapTracker
-
- Cli - Class in gngs
This class is a simple utility that configures a CliBuilder how I like it and adds a few
simple options that I like.
- Cli() - Constructor in Cli
-
- cli(java.lang.String, java.lang.String, java.lang.String, groovy.lang.Closure) - Method in ToolBase
-
Create an instance of the enclosing class and call its
run method after
parsing options with a
Cli instance configured by
the provided
specBiulder closure.
- ClinVar - Class in ClinVar
A thin wrapper around a RangedData object to add some utility functions
for accessing clinvar data.
- clinvar - Property in ClinVar
-
- CLINVAR_COLUMNS - Property in ClinVar
-
Columns from schema of clinvar in UCSC table
- clinvarFile - Property in ClinVar
-
- CliOptions - Class in gngs
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.
- CliOptions() - Constructor in CliOptions
-
- close() - Method in AsciiWriter
-
flushes and closes underlying OutputStream.
- close() - Method in OrderedPairReader
-
- close() - Method in OrderedPairWriter
-
- close() - Method in Pileup
-
- close() - Method in PileupIterator
-
- close() - Method in SAM
-
Close the underlying SamReader
- close() - Method in VariantDB
-
- CNVDatabase - Class in gngs
Abstract interface that can be implemented by different
CNV sources.
- CNVDatabase() - Constructor in CNVDatabase
-
- cnvDatabases - Property in TargetedCNVAnnotator
-
- CNVFrequency - Class in gngs
- CNVFrequency() - Constructor in CNVFrequency
-
- CODING_SEQUENCE_VARIANT - Field in VepConsequence
-
- coeffV - Property in CoverageSummary
-
- color(java.lang.String, groovy.lang.Closure) - Method in PDF
-
- colors - Property in Palette
-
- COLUMN_NAMES - Property in RefGenes
-
- columnNames - Property in BED
-
- columns - Property in GATKIntervalSummary
-
- columns - Property in RangedData
-
- CompactReadPair - Class in gngs
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.
- CompactReadPair.ReadCompressor - Interface in gngs
- CompactReadPair(htsjdk.samtools.SAMRecord, java.lang.String) - Constructor in CompactReadPair
-
Create a compact read pair that encodes base qualities extracted from the given tag.
- compare(gngs.pair.Paired, gngs.pair.Paired) - Method in PairedReadComparator
-
- compare(groovy.lang.IntRange, groovy.lang.IntRange) - Method in RangeIndex.1
-
- compareTo(java.lang.Object) - Method in VCFMergeSource
-
- complement - Property in RestrictionEnzyme
-
- compress(byte[], byte[]) - Method in CompactReadPair.ReadCompressor
-
- compressedBases - Field in CompactReadPair
-
- compute() - Method in VCFSimilarity
-
- computeExonicRegions(List<String>) - Method in GeneCovStats
-
- computeId(int, int) - Method in XPos
-
- computeKmer(htsjdk.samtools.SAMRecord) - Method in ShearingKmerCounter
-
- computeMaxRange(gngs.IRegion) - Method in TargetedCNVAnnotator
-
- computePos(java.lang.String, int) - Method in XPos
-
- computeReplacementBases() - Method in VariantInjector
-
Computes the corresponding sequence after a reference sequence is mutated by a variant
which must be a SNV, insertion or deletion
- concurrency - Property in ExtractFASTQ
-
- connectString - Property in VariantDB
-
The file name of the database that is connected to
- CONSANGUINEOUS - Field in Consanguinity
-
- Consanguinity - Enum in gngs.sample
- consanguinity - Property in SampleInfo
-
Whether the sample is consanguinous
- consensus - Property in BaseCounts
-
- Constraint - Interface in gngs
Represents a constraint in a genetic model
- contains(java.lang.String, int) - Method in Regions
-
Return true iff the given chromosome and position fall into
a range covered by this BED file
- contains(gngs.Variant) - Method in VCFIndex
-
Returns true if this VCF contains the specified variant
- contigs - Property in MergePartitionedVCFs
-
- continueRunning - Property in CoveragePrinter
-
- count - Property in ProgressCounter
-
- count - Property in ReadSpans
-
- countInfo - Property in CoverageSummary
-
- countMotifs(htsjdk.samtools.SAMRecordIterator) - Method in ShearingKmerCounter
-
- countObservations(gngs.Variant, gngs.Variant$Allele) - Method in VariantDB
-
Return a counts of the number of observations of the given variant.
- countOf(byte) - Method in Pileup
-
Return the count of reads supporting the specified base at the current
position.
- countOf(Closure<Object>) - Method in PileupIterator.Pileup
-
- countOf(java.lang.String, int, java.lang.String) - Method in SAM
-
- countOnTarget(gngs.Regions) - Method in SAM
-
Return a set of read counts indicating the counts of reads in that overlap the target region.
- countPairs(java.lang.String, int, int) - Method in SAM
-
Count the number of read pairs in the given region
- countReads() - Method in TargetedCoverageCalculator
-
Return an integer array containing the number of reads overlapping each of the intervals
in the bam file.
- counts - Property in PositionCounts
-
- countSplitReads(gngs.SAM) - Method in DeletionPlot
-
- coverage(gngs.Region) - Method in BEDToolsCoverage
-
- coverage() - Method in RangeIndex
-
Return a list of ranges representing "coverage" blocks within this
index.
- coverage() - Method in Regions
-
Return a new regions object that has each distinct region of this object
with a "coverage" value assigned.
- coverage(htsjdk.samtools.SamReader, java.lang.String, int, int, groovy.lang.Closure, int) - Method in SAM
-
Return the number of mapped reads overlapping the given position
- coverageAsync(gngs.Regions, gngs.RegulatingActor, int) - Method in SAM
-
- CoverageBlock - Class in gngs
A run of contiguous bases within a band of coverage depth
(eg: a run of low coverage bases).
- CoverageBlock() - Constructor in CoverageBlock
-
- CoverageDownsampler - Class in gngs.coverage
Accepts SampleReadCount objects as messages and calculates a moving window
of their values, emitting the window mean instead of the original
values.
- CoverageDownsampler(RegulatingActor<SampleReadCount>, int, int) - Constructor in CoverageDownsampler
-
- coverageFilePath - Property in CoverageGaps
-
- CoverageGaps - Class in gngs
Discovers blocks of low coverage in a file output in BEDTools Coverage format,
or alternatively
MultiCov output.
- CoverageGaps(java.lang.String) - Constructor in CoverageGaps
-
- coveragePercentiles - Property in CoverageGaps
-
- CoveragePosition - Class in gngs.tools
- CoveragePosition(java.lang.String, int, List<Integer>) - Constructor in CoveragePosition
-
- CoveragePrinter - Class in gngs.coverage
- CoveragePrinter(java.io.Writer) - Constructor in CoveragePrinter
-
- coverageStatistics(gngs.Regions) - Method in SAM
-
- CoverageStats - Class in gngs
An efficient method to calculate percentiles of coverage values
that doesn't require holding them all in memory or sorting them.
- coverageStats - Property in CoverageGaps
-
- CoverageStats(int) - Constructor in CoverageStats
-
- CoverageSummary - Class in gngs.coverage
- CoverageSummary(gngs.coverage.PositionCounts, List<Double>, java.lang.Double, java.lang.Double) - Constructor in CoverageSummary
-
- covs - Property in BEDToolsCoverage
-
- covs - Property in Delfin
-
- CREATE_SAMPLE_SQL - Property in Schema
-
- createCoverageStats() - Method in DeletionPlot
-
- createFather(java.lang.String) - Method in Subject
-
- createLocator(gngs.SAM, Set<Integer>, gngs.pair.Shuffler) - Method in PairScanner
-
- createMother(java.lang.String) - Method in Subject
-
- currentChr - Property in OrderedPairReader
-
- currentFont - Property in PDF
-
- currentReferenceIndex - Property in OrderedPairWriter
-
- currentRegion - Property in OrderedPairReader
-
- currentTable - Property in PDF
-
- CustomInfo - Class in gngs.tools
- CustomInfo() - Constructor in CustomInfo
-
- cutsSequenceBefore(java.lang.String, int) - Method in RestrictionEnzyme
-
Returns true if this restriction enzyme would cut the given sequence
in between the given position and the previous position.
- cvThresholds - Property in MultiCov
-
- families - Property in Pedigrees
-
Lookup table to find family by family Id
- FASTAIndex - Class in gngs
A very simplistic FASTA index that allows lookup of sequence names by their
sequence content using a fixed length prefix seed.
- FASTAIndex(gngs.FASTA, groovy.lang.IntRange, int, int, gngs.BED) - Constructor in FASTAIndex
-
Create an index from the given fasta, where each fasta sequence corresponds
to a single amplicon
- FASTHRead - Class in gngs
Models a single FASTH read, including the header (with name), barcodes, bases and
quality information.
- FASTHRead(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String) - Constructor in FASTHRead
-
- FASTQDedupeActor - Class in gngs.tools
- FASTQDedupeActor(gngs.RegulatingActor) - Constructor in FASTQDedupeActor
-
- FastQIdent - Class in gngs.tools
Find sequences not present in a raw fastq file
- FastQIdent() - Constructor in FastQIdent
-
- father - Property in PedTrio
-
- fatherOf(java.lang.String) - Method in Pedigrees
-
- Feature - Class in gngs.gencode
- FEATURE_ELONGATION - Field in VepConsequence
-
- Feature(gngs.IRegion, java.lang.String, gngs.gencode.Feature) - Constructor in Feature
-
- FEATURE_TRUNCATION - Field in VepConsequence
-
- features - Property in Gencode
-
- FEMALE - Field in Sex
-
- fields - Property in OMIM
-
- file - Property in GATKIntervalSummary
-
- fileMappings - Property in SampleInfo
-
- fileName - Property in VCFIndex
-
File name of VCF file
- files - Property in SampleInfo
-
List of files containing data specific to this sample, indexed by file types:
- fastq
- coverage (output from coverageBed)
- vcf
- bam
- cram
- fillRelationships(gngs.Pedigree) - Method in SamplesToPed
-
Fill in all the relationship ids on the assumption that they are
relative to a single affected child.
- filter - Property in FASTQDedupeActor
-
- filter - Property in FastQIdent
-
- filter(java.util.Map, java.lang.String, groovy.lang.Closure) - Method in SAM
-
Filter the SAM/BAM file to include only the reads for which the given closure returns true
- filterByType(java.lang.String, List<Region>) - Method in DGV
-
- filterByType(java.lang.String, List<Region>) - Method in TargetedCNVAnnotator
-
- filterClosure - Property in PairFilter
-
- filterExpr - Property in PairScanner
-
- filterOrderedPairs(java.util.Map, java.lang.String, groovy.lang.Closure) - Method in SAM
-
Execute the given closure with an actor (parallel thread) set to write ordered
pairs to the given output file, based on this BAM file.
- filters - Property in PairScanner
-
- filterToBAMContigs(gngs.Regions) - Method in MultiCov
-
- find(java.lang.String, int, int, groovy.lang.Closure) - Method in VCFIndex
-
Find the first variant in an interval that returns true from the
given closure
- findAnnovarVariant(java.lang.String, java.lang.Object, java.lang.Object, java.lang.String, int) - Method in VCFIndex
-
Attempts to locate the given Annovar variant in this VCF file.
- findCompatibleRanges(gngs.CNVDatabase, gngs.IRegion) - Method in TargetedCNVAnnotator
-
- FindCompoundHets - Script in FindCompoundHets
- FindCompoundHets(groovy.lang.Binding) - Constructor in FindCompoundHets
-
- findDifferences() - Method in VEPDiff
-
Return a list of maps containing identical variants having different VEP consequences or features
between the two VCFs
- findMaximalUnrelatedSet(java.lang.String) - Method in Pedigrees
-
Find the largest possible set of samples that are unrelated to
the given sample.
- findNext() - Method in RangeIndex.2
-
- findNext() - Method in RangeIndex.3
-
- findSample(java.lang.String) - Method in VariantDB
-
Return row of database representing sample, or null if it does not
exist.
- findVariant(gngs.Variant, gngs.Variant$Allele) - Method in VariantDB
-
Find a variant in the database by its start position
- first() - Method in RangeIndex
-
- FIVE_PRIME_UTR_VARIANT - Field in VepConsequence
-
- flags - Property in Paired
-
- flush() - Method in AsciiWriter
-
flushes underlying OutputStream
- flush(RegulatingActor<T>) - Method in BatchedAcknowledgeableMessage
-
- flushBuffer() - Method in OrderedPairWriter
-
- flushBuffer() - Method in PairFormatter
-
- flushBufferAndWriter(java.lang.StringBuilder, gngs.pair.PairWriter) - Method in PairFormatter
-
- flushSpooledReads(groovy.lang.Closure) - Method in OrderedPairReader
-
- fmt - Property in MultiCov
-
- font(java.awt.Color, int, groovy.lang.Closure) - Method in PDF
-
- fontSize(float, groovy.lang.Closure) - Method in PDF
-
- fontStack - Property in PDF
-
- footer - Property in ToolBase
-
- forcedQueries - Property in OrderedPairReader
-
- forcedQueryLookupActor - Property in OrderedPairReader
-
- forceQueryOverflowRead(int) - Method in OrderedPairReader
-
- format(LogRecord) - Method in SimpleLogFormatter
-
A Custom format implementation that is designed for brevity.
- FormatMetaData - Class in gngs
- FormatMetaData() - Constructor in FormatMetaData
-
- formatted - Property in PairFormatter
-
- FORMATTER_BUFFER_SIZE - Property in PairScanner
-
The size of blocks to format before writing.
- formatterGroup - Property in PairScanner
-
- formatters - Property in PairScanner
-
- forward(java.lang.String, int, int) - Method in Regions
-
Returns the region that is count regions forward of the given position
- forwardPrefix - Property in RestrictionEnzyme
-
- forwardPrefixPattern - Property in RestrictionEnzyme
-
- forwardSuffix - Property in RestrictionEnzyme
-
- forwardSuffixPattern - Property in RestrictionEnzyme
-
- fractionAbove(int) - Method in CoverageStats
-
- FRAMESHIFT_VARIANT - Field in VepConsequence
-
- from - Property in LiftOver
-
- fromFiles(List<String>, java.lang.String) - Method in SampleInfo
-
Create a list of SampleInfo objects from provided files that
contain sample information in the header data.
- fromSingletons(List<String>) - Method in Pedigrees
-
A convenience method that creates a set of pedigrees from set of
unrelated singletons.
- fromTerm(java.lang.String) - Method in VepConsequence
-
- G - Field in BaseCompactor
-
- g - Property in BaseCounts
-
- GapAnnotator - Class in gngs.tools
Annotates regions with gene, transcript, CDS overlap and distance information, as well
as custom annotation to gene associations ("panels") and sub-panels
(groups of genes within a panel)
- GapAnnotator(RefGenes, ArrayList<String>) - Constructor in GapAnnotator
-
- gapProcessor - Property in CoverageGaps
-
- GATKIntervalSummary - Class in gngs
Reads output of GATK DepthOfCoverage interval summary and
makes it available as a Regions object
- GATKIntervalSummary(java.lang.String) - Constructor in GATKIntervalSummary
-
- GATKMeans - Class in gngs
Estimates sample means by reading interval summary file output by GATK
- GATKMeans(java.lang.String) - Constructor in GATKMeans
-
- gcScore - Property in IlluminaSNPData
-
- Gencode - Class in gngs.gencode
Class implementing parsing of Gencode GFF3 format
- Gencode(java.lang.Object) - Constructor in Gencode
-
- gene - Property in OMIM
-
- gene - Property in SnpEffInfo
-
The gene impacted (if any) by the variant
- GeneAnnotationSource - Interface in gngs
Abstract interface for gene annotation sources
- geneCategories - Property in SampleInfo
-
List of genes prioritised for the sample
- GeneCovStats - Class in gngs.tools
- GeneCovStats() - Constructor in GeneCovStats
-
- GENEMAP2_FIELDS - Field in OMIM
-
- generateRandomSamplingRegions() - Method in MeanCoverageEstimator
-
- geneRegions - Property in Gencode
-
- genes - Property in Gencode
-
- geneToTranscripts - Property in RefGenes
-
Transcripts indexed by gene
- GenomeInfo - Class in gngs
Static constant information about various genomes used to enable auto-sniffing etc
- GenomeInfo() - Constructor in GenomeInfo
-
- genomeMappings - Property in LiftOver
-
- GenomeResource - Class in gngs
- GenomeResource() - Constructor in GenomeResource
-
- genomeZeroOffset - Property in RangedData
-
The starting index for the first base in the genome.
- Genotype - Class in gngs.tools
A simple tool that measures the status of predefined SNPs in a
a BAM file, where SNPs are provided as a VCF file.
- Genotype() - Constructor in Genotype
-
- genotype(java.lang.String, int) - Method in SAM
-
Use a simple thresholding approach to genotype SNPs at the given location
- getAbort() - Method in ProgressCounter
-
- getAccessTokenEndpoint() - Method in TwoLeggedOAuthAPI
-
- getAffected() - Method in Pedigrees
-
- getAlignments() - Method in PileupIterator.Pileup
-
- getAlleleNumber(gngs.Sex, java.lang.String) - Method in AlleleNumber
-
- getAllSubjects() - Method in Pedigrees
-
- getAllValues(int) - Method in TrieNode
-
- getAlternateAlignments(htsjdk.samtools.BAMRecord) - Method in SAMRecordCategory
-
- getAnnotation(java.lang.String, java.lang.Object) - Method in VariantDB
-
Search for the given value in the annotations as a frequency
value.
- getAt(java.lang.String) - Method in Pedigrees
-
Get Subject by their id
- getAt(java.lang.String) - Method in PrefixTrie
-
- getAt(java.lang.Object) - Method in Regions
-
- getAt(java.lang.String) - Method in TrieNode
-
- getAtIndex(java.lang.Object) - Method in Regions
-
- getAuthorizationBaseUrl() - Method in TwoLeggedOAuthAPI
-
- getBAMSamples(java.lang.String) - Method in SampleInfo
-
- getBoundaries() - Method in RangeIndex
-
Returns a range for each boundary within the index.
- getCDS(gngs.IRegion) - Method in GeneAnnotationSource
-
Compute a map of gene symbols with the amount of coding sequence overlapped by each gene
for the given region
- getCDS(gngs.IRegion) - Method in RefGenes
-
Compute a map of gene symbols with the amount of coding sequence overlapped by each gene
for the given region
- getChildren() - Method in Feature
-
- getChr() - Method in IRegion
-
- getConsensus() - Method in BaseCounts
-
- getConsequence() - Method in SnpEffInfo
-
This is an alias for the SNPEFF 'type' which is useful when trying to make
code use both SNPEFF and VEP annotations
- getContigList() - Method in SAM
-
- Returns:
- a list of contigs in the BAM file in sort order of the BAM file
- getContigRegions(java.lang.String) - Method in Regions
-
- getContigRegions() - Method in SAM
-
Return the contigs of this BAM file as a set of regions
- getContigs() - Method in SAM
-
- Returns:
- Map of contig name to size for all the contigs in this SAM
- getContigsWithReads(gngs.SAM) - Method in PairScanner
-
Interrogate the BAM index to determine which contigs have reads.
- getExons(java.lang.String) - Method in GeneAnnotationSource
-
- Returns:
- list of regions representing flattened exons (all transcripts) of the given gene
- getExons(gngs.IRegion) - Method in RefGenes
-
- getExonsForTranscript(java.lang.String) - Method in GapAnnotator
-
- getExtrasAtPosition(java.lang.String, int) - Method in Regions
-
- getFemales() - Method in Pedigrees
-
- getFreq(java.lang.String, java.lang.Object) - Method in VariantDB
-
Search for the given value in the annotations as a frequency
value.
- getGeneRegion(java.lang.String) - Method in Gencode
-
- getGeneRegion(java.lang.String) - Method in RefGenes
-
Look up the entire span of a gene from its HGNC symbol
- getGeneRegions(java.lang.String, List<String>) - Method in ExtractFASTQ
-
Attempt to interpret the given list of genes as either a list of gene symbols
or a text file specifying the genes to read.
- getGenes(gngs.IRegion) - Method in GeneAnnotationSource
-
- Returns:
- the list of all gene symbols overlapping the given region
- getGenes(gngs.IRegion) - Method in RefGenes
-
- Parameters:
region - the region to query
- getMales() - Method in Pedigrees
-
- getMinMappingQuality() - Method in PileupIterator
-
- getNumberOfRanges() - Method in Regions
-
- getNumRanges() - Method in RangeIndex
-
- getOverlapRegions(gngs.IRegion) - Method in Regions
-
Returns the overlaps with with the given region as region objects.
- getOverlaps(int, int, boolean) - Method in RangeIndex
-
Return a list of the ranges in this index that overlap the given range.
- getOverlaps(java.lang.String, int, int) - Method in Regions
-
Return a list of ranges that overlap the specified range.
- getPanelAnnotations(java.lang.String) - Method in GapAnnotator
-
- getParentIds() - Method in Subject
-
- getProperty(java.lang.String) - Method in CliOptions
-
- getR1NegativeStrandFlag() - Method in Paired
-
- getR2NegativeStrandFlag() - Method in Paired
-
- getRange() - Method in CoverageBlock
-
- getRange() - Method in IlluminaSNPData
-
- getRange() - Method in IRegion
-
- getRank() - Method in VepConsequence
-
- getReader(java.lang.String) - Method in RangedData
-
- getReadGroups() - Method in SAM
-
- Returns:
- Return the list of read groups present in the SAM file
- getReadIterator() - Method in PileupIterator
-
- getReadLength() - Method in CompactReadPair
-
- getRegions() - Method in Pairs
-
- getReorderRequired() - Method in Paired
-
- getRequestTokenEndpoint() - Method in TwoLeggedOAuthAPI
-
- getSamples() - Method in SAM
-
- getScore() - Method in BaseCounts
-
- getSeverity() - Method in VepConsequence
-
- getShortName() - Method in VepConsequence
-
- getSpan(java.lang.String) - Method in Regions
-
Returns the total span from the beginning of the first region to the end of
the last region on the given contig (chromosome).
- getSpliceSites(java.lang.String) - Method in RefGenes
-
Return a regions object containing a region for each unique exon in the transcript.
- getSubjectsBySex(gngs.Sex) - Method in Pedigrees
-
- getSummary() - Method in Pileup
-
Returns a summary of the coverage at the location:
- getSummary() - Method in PileupIterator.Pileup
-
Returns a summary of the coverage at the location:
- getSummaryAsMap() - Method in Pileup
-
Convenience method to return counts of each base as a map indexed
by the base as a string.
- getSummaryAsMap() - Method in PileupIterator.Pileup
-
Convenience method to return counts of each base as a map indexed
by the base as a string.
- getTotalSize() - Method in RepeatMotif
-
- getTranscriptExons(java.lang.String) - Method in RefGenes
-
- getTranscriptIds(java.lang.String) - Method in RefGenes
-
Return the names of all the transcripts (NM_... identifiers) for the
given HGNC symbol
- getTranscripts(java.lang.String) - Method in RefGenes
-
Return a list of transcript objects as Regions having all the
full properties of a transcript (see COLUMN_NAMES)
- getUnaffected() - Method in Pedigrees
-
- getUnmapped() - Method in CompactReadPair
-
- getUnmapped() - Method in ReadPair
-
- getVariantSet(gngs.VCF, java.lang.String) - Method in VCFSimilarity
-
- getVCFSamples(java.lang.String) - Method in SampleInfo
-
- global(java.util.Map, java.lang.String, java.lang.String) - Method in Align
-
Returns a BioJava aligner with profile computed.
- gnomad - Property in GnomADCNVDatabase
-
- GnomADCNVDatabase - Class in gngs
A
CNVDatabase implementation for CNVs from the gnomAD
sv dataset.
- GnomADCNVDatabase(gngs.VCFIndex) - Constructor in GnomADCNVDatabase
-
- GnomADHist - Class in gngs
- GnomADHist() - Constructor in GnomADHist
-
- grcMap - Property in GenomeInfo
-
- gtScore - Property in IlluminaSNPData
-
- guessFastqSex(java.lang.String) - Method in Sex
-
- p(java.lang.String) - Method in PDF
-
- padding - Property in MeanCoverageEstimator
-
- padding - Property in VariantInjector
-
- pair - Property in ResolveRequest
-
- Paired - Class in gngs.pair
- Paired(java.lang.String, PairType, PairType, boolean, boolean, boolean, int) - Constructor in Paired
-
- PairedReadComparator - Class in gngs.pair
- PairedReadComparator() - Constructor in PairedReadComparator
-
- PairFilter - Class in gngs.pair
- PairFilter(RegulatingActor<Paired>, java.lang.String) - Constructor in PairFilter
-
- PairFormatter - Class in gngs.pair
Converts reads to FASTQ format, and sends them in batches to a writer.
- PairFormatter(int, gngs.pair.PairWriter, gngs.pair.PairWriter) - Constructor in PairFormatter
-
- Pairs - Class in gngs.tools
Extracts read pairs from BAM or CRAM files sorted in coordinate order.
- pairs - Property in OrderedPairReader
-
- Pairs() - Constructor in Pairs
-
- PairScanner - Class in gngs.pair
Scans a BAM file and feeds reads encountered to a pool of gngs.pair.PairLocator
instances for matching to pairs.
- PairScanner(java.io.Writer, int, gngs.Regions, java.lang.String, int) - Constructor in PairScanner
-
- PairWriter - Class in gngs.pair
A simple class that whose purpose is purely to paralleise
writing output to a Writer.
- pairWriter2 - Property in PairScanner
-
- pairWriter - Property in PairScanner
-
- PairWriter(java.io.Writer, int) - Constructor in PairWriter
-
- Palette - Class in gngs.plot
- Palette() - Constructor in Palette
-
- panelClasses - Property in GapAnnotator
-
List of all known sub panels ("panel classes")
- panelGeneMap - Property in GapAnnotator
-
Map keyed on gene to a nested lookup table that is keyed on panel name and returns the list of
subpanels from the major panel that include the gene.
- parent - Property in Feature
-
- parse10XWhitelist(java.lang.String) - Method in SplitFASTQ10X
-
- parse10XWhitelist(java.lang.String) - Method in TrimBarcode10X
-
- parse(java.lang.String) - Method in BED
-
- parse() - Method in ClinVar
-
- parse() - Method in DecipherCNVs
-
- parse() - Method in DGV
-
Parse the data source set for this database
- parse(java.lang.Object, java.lang.Object, java.lang.Object) - Method in GnomADHist
-
- parse(java.lang.String) - Method in IlluminaFileNameParser
-
Examples of the various formats we try to parse:
- parse_mg_sample_info(java.lang.String) - Method in SampleInfo
-
Parse the given file to extract sample info, where the file is in the
extended Melbourne Genomics Health Alliance format.
- parse(java.lang.String) - Method in OMIM
-
- parse(java.io.Reader, groovy.lang.Closure) - Method in Pedigrees
-
Parse a PED file from the given reader, with optional filtering via the provided closure
- parse(java.lang.String) - Method in PicardMetrics
-
- parse_sample_info(java.lang.String, java.util.List) - Method in SampleInfo
-
Parse the given file to extract sample information
- parseDate(java.lang.String) - Method in SampleInfo
-
- parsePos(long) - Method in XPos
-
- parser - Property in ToolBase
-
- parseRegion(com.xlson.groovycsv.PropertyMapper) - Method in RangedData
-
- path - Property in GenomeResource
-
- payload - Field in AcknowledgeableMessage
-
- PDF - Class in gngs
A light weight PDF Builder for creating PDFs to show results.
- PDF() - Constructor in PDF
-
- PED_COLUMNS - Property in Pedigrees
-
- pedigree - Property in SampleInfo
-
The pedigree of the family
- Pedigrees - Class in gngs
- Pedigrees() - Constructor in Pedigrees
-
- PedTrio - Class in gngs.tools
- PedTrio() - Constructor in PedTrio
-
- pending - Property in OrderedPairActor
-
- pending - Field in PairWriter
-
- pending - Property in VCFWalkPosition
-
- pendingMessageCount - Property in RegulatingActor
-
Count of messages that have been sent to this actor but not processed
- phase1 - Property in MultiCov
-
- Phenotype - Class in Phenotype
- Phenotype() - Constructor in Phenotype
-
- phenoTypes - Property in Subject
-
- PicardMetrics - Class in PicardMetrics
A simple class for parsing information out of the metrics file written by Picard
- PicardMetrics() - Constructor in PicardMetrics
-
- Pileup - Class in gngs
Overall class containing pileup state
- Pileup(htsjdk.samtools.SamReader, java.lang.String, int, int) - Constructor in Pileup
-
- pileup(htsjdk.samtools.SamReader, java.lang.String, int, int) - Method in SAM
-
- PileupIterator - Class in gngs
Overall class containing pileup state
- PileupIterator.Pileup - Class in gngs
Inner class that captures pileup state at a specific position
- PileupIterator(htsjdk.samtools.SamReader, java.lang.String, int, int) - Constructor in PileupIterator
-
- PileupState - Class in gngs
Additional state about a read that is part of a pileup
- plot_chr(gngs.VCF, java.lang.String) - Method in LCSHPlot
-
- plotCoverage() - Method in DeletionPlot
-
- plotSplitReads() - Method in DeletionPlot
-
- plus(gngs.Regions) - Method in Regions
-
- pos - Property in CoveragePosition
-
- pos - Property in IlluminaSNPData
-
- pos - Property in PositionCounts
-
- pos - Property in RangeIndex.2
-
- pos - Property in RangeIndex.3
-
- pos - Property in ReadWindow
-
The of the window
- pos - Property in SampleReadCount
-
- pos - Property in XA
-
- position - Field in Pileup
-
- position - Field in PileupIterator.Pileup
-
- position - Property in RepeatMotif
-
- PositionCounts - Class in gngs.coverage
- PositionCounts(gngs.Region, int, Map<String, Integer>) - Constructor in PositionCounts
-
- prefix - Property in ProgressCounter
-
- PrefixTrie - Class in gngs
- PrefixTrie() - Constructor in PrefixTrie
-
- preprocessedReads - Property in OrderedPairReader
-
- prev - Property in RangeIndex.4
-
- previous() - Method in Consanguinity
-
- previous() - Method in Ethnicity
-
- previous() - Method in IlluminaFileNameParser.DIALECT
-
- previous() - Method in SampleType
-
- previous() - Method in Sex
-
- previous() - Method in VepConsequence
-
- previousRange(int) - Method in RangeIndex
-
- previousRange(java.lang.String, int) - Method in Regions
-
Returns the prior range that has its end closest
to the given position.
- prevRange - Property in RangeIndex.3
-
- prevRange - Property in RangeIndex.4
-
- primaryRegion - Property in AltContig
-
- printTitle() - Method in ToolBase
-
- proband - Property in PedTrio
-
- process(gngs.coverage.SampleReadCount) - Method in CoverageDownsampler
-
- process(gngs.coverage.CoverageSummary) - Method in CoveragePrinter
-
- process(java.lang.Object) - Method in FASTQDedupeActor
-
- process(gngs.CoverageBlock) - Method in GapAnnotator
-
- process(gngs.pair.Paired) - Method in PairFilter
-
- process(gngs.pair.Paired) - Method in PairFormatter
-
- process(Map<String, Object>) - Method in PairWriter
-
- process(T) - Method in RegulatingActor
-
- process(T) - Method in RegulatingActor.2
-
- process(gngs.coverage.SampleReadCount) - Method in SexKaryotyper.1
-
- processBAM(java.lang.String) - Method in Sex
-
- processLine(java.lang.String, int, int, int, java.lang.String) - Method in CoverageGaps
-
- processParallelBAMs(List<String>) - Method in Sex
-
- processPartneredReads(groovy.lang.Closure) - Method in OrderedPairReader
-
- profile(java.lang.String, java.lang.String) - Method in Align
-
Returns a formatted string representing the comparison between the two sequences
with '-' representing gaps and '|' joining mismatches.
- progress - Property in AsyncMateResolveWorker
-
- progress - Property in CoveragePrinter
-
- progress - Property in Gencode
-
- progress - Property in OrderedPairReader
-
- progress - Property in OrderedPairWriter
-
- progress - Property in PairScanner
-
- progress - Property in RegulatingActor
-
- progress - Property in SAM
-
- progress - Property in SexKaryotyper
-
- ProgressCounter - Class in gngs
Simple utility for displaying progress
- ProgressCounter() - Constructor in ProgressCounter
-
- PROTEIN_ALTERING_VARIANT - Field in VepConsequence
-
- r1 - Field in Paired
-
- R1_READ_NEGATIVE_STRAND_FLAG - Property in Paired
-
- r1AlignmentStart - Field in CompactReadPair
-
- r1bases - Property in FASTHRead
-
- r1quals - Property in FASTHRead
-
- r1ReferenceName - Field in CompactReadPair
-
- r2 - Field in Paired
-
- R2_READ_NEGATIVE_STRAND_FLAG - Property in Paired
-
- r2AlignmentStart - Field in CompactReadPair
-
- r2bases - Property in FASTHRead
-
- r2quals - Property in FASTHRead
-
- r2ReferenceName - Field in CompactReadPair
-
- R - Property in IlluminaSNPData
-
- random - Property in MeanCoverageEstimator
-
- randomLookupReader - Property in OrderedPairReader
-
- range - Property in Feature
-
- RangedData - Class in gngs
RangedData represents a set of genomic regions with data attached.
- RangedData(graxxia.ReaderFactory, int, int, int) - Constructor in RangedData
-
- RangeIndex - Class in gngs
Indexes a set of ranges so that the ranges crossing any point
can be identified quickly and easily.
- RangeIndex.1 - Class in gngs
- RangeIndex.1() - Constructor in RangeIndex.1
-
- RangeIndex.2 - Class in gngs
- RangeIndex.2() - Constructor in RangeIndex.2
-
- RangeIndex.3 - Class in gngs
- RangeIndex.3() - Constructor in RangeIndex.3
-
- RangeIndex.4 - Class in gngs
- RangeIndex.4() - Constructor in RangeIndex.4
-
- RangeIndex() - Constructor in RangeIndex
-
- ranges - Property in RangeIndex
-
The actual index - a map from position to the list of ranges
covering the region after the position.
- read - Field in PileupState
-
- readColumnNames - Property in BED
-
- ReadPair - Interface in gngs
- readPatiently(java.io.Reader) - Method in SplitLiveFASTQ
-
- ReadRange - Class in gngs.coverage
- ReadRange(htsjdk.samtools.SAMRecord, boolean) - Constructor in ReadRange
-
- reads - Field in OverlapTracker
-
- reads - Property in SampleReadCount
-
- readSampleInfoLines(java.lang.String) - Method in SampleInfo
-
- ReadSpans - Class in gngs.tools
- ReadSpans() - Constructor in ReadSpans
-
- readVCF(java.lang.String, int) - Method in MergePartitionedVCFs
-
- ReadWindow - Class in gngs
Models a window positioned centrally around a location in the genome containing overlapping reads
- ReadWindow() - Constructor in ReadWindow
-
- red(groovy.lang.Closure) - Method in PDF
-
- reduce(groovy.lang.Closure) - Method in RangeIndex
-
Merge all overlapping ranges together to make simplified regions
representing all the ranges covered by any range in this RangeIndex.
- reduce(groovy.lang.Closure) - Method in Regions
-
Simplify all overlapping regions down to a single region, with an optional
closure as a callback to combine the attributes of combined regions
- refData - Property in RefGenes
-
- reference - Property in VariantInjector
-
- referenceBases - Property in VariantInjector
-
- referenceBasesRC - Property in VariantInjector
-
- referenceIndex - Field in ReadRange
-
- referenceName - Field in ReadRange
-
- refGene - Property in GeneCovStats
-
- RefGenes - Class in gngs
A convenience class that is set up to parse the UCSC RefGene database
as a RangedData object.
- refgenes - Property in GapAnnotator
-
- RefGenes(java.io.Reader) - Constructor in RefGenes
-
- region - Property in CoverageBlock
-
- region - Property in CoverageGaps
-
- region - Property in PositionCounts
-
- region - Field in ScannableRegion
-
- RegionIterator - Class in gngs
- regionParser - Property in RangedData
-
- Regions - Class in gngs
A set of genomic regions, each indexed by chromosome, start and end position.
- regions - Property in CoverageGaps
-
- regions - Property in ExtractFASTQ
-
- regions - Property in MeanCoverageEstimator
-
- regions - Property in PairScanner
-
- Regions(java.util.Map, Iterable<IRegion>) - Constructor in Regions
-
Create a Regions from a list of regions
- regions - Property in SexKaryotyper
-
- regions - Property in TargetedCoverageCalculator
-
- regionsEndingAt(java.lang.String, int) - Method in Regions
-
Return a list of ranges that end exactly at the specified position.
- regionsStartingAt(java.lang.String, int) - Method in Regions
-
- RegulatingActor - Class in gngs
An Actor that exerts back-pressure to regulate the rate of incoming messages.
- RegulatingActor.1 - Class in gngs
- RegulatingActor.1() - Constructor in RegulatingActor.1
-
- RegulatingActor.2 - Class in gngs
- RegulatingActor.2() - Constructor in RegulatingActor.2
-
- RegulatingActor() - Constructor in RegulatingActor
-
Create a RegulatingActor with basic defaults for the queue sizes that suit many tasks
- REGULATORY_REGION_ABLATION - Field in VepConsequence
-
- REGULATORY_REGION_AMPLIFICATION - Field in VepConsequence
-
- REGULATORY_REGION_VARIANT - Field in VepConsequence
-
- relationships - Property in Subject
-
- remove() - Method in Pileup
-
- remove() - Method in PileupIterator
-
- remove(groovy.lang.Range) - Method in RangeIndex
-
Remove an existing range from the index.
- remove() - Method in RangeIndex.2
-
- remove() - Method in RangeIndex.3
-
- remove() - Method in RangeIndex.4
-
- remove() - Method in RegionIterator
-
- remove(java.lang.String, groovy.lang.Range) - Method in Regions
-
- remove() - Method in VCFIndex.1
-
- removeFamily(java.lang.String) - Method in Pedigrees
-
- removeNonOverlaps(int) - Method in OverlapTracker
-
- renameFamily(java.lang.String, java.lang.String) - Method in Pedigrees
-
- renameRead(gngs.FASTQRead, gngs.FASTQRead) - Method in VariantInjector
-
- renameSubject(java.lang.String, java.lang.String) - Method in Pedigrees
-
- rendering - Property in CustomInfo
-
- REORDER_IN_OUTPUT - Property in Paired
-
- RepeatMotif - Class in gngs
- RepeatMotif() - Constructor in RepeatMotif
-
- repetitions - Property in RepeatMotif
-
- replacementBases - Property in VariantInjector
-
- replacementBasesRC - Property in VariantInjector
-
- resolveAsynchronously(gngs.SAMRecordPair) - Method in OrderedPairReader
-
- resolveRegionsToScan() - Method in MultiCov
-
Combine the various possible options for specifying which region to analyse
into a single regions object (see
scanRegions).
- ResolveRequest - Class in gngs
- ResolveRequest() - Constructor in ResolveRequest
-
- resolvers - Property in OrderedPairReader
-
- RestrictionEnzyme - Class in RestrictionEnzyme
A simple class for matching motifs in restriction enzymes to
FASTA sequence.
- RestrictionEnzyme(java.lang.String, java.lang.String, int, int, boolean) - Constructor in RestrictionEnzyme
-
Create a restriction enzyme object with given name, motif cut point and overhang.
- results - Property in Delfin
-
- reverse_translation - Property in ShearingKmerCounter
-
- reverseIterator() - Method in RangeIndex
-
- reverseIteratorAt(int) - Method in RangeIndex
-
Return an iterator that will return each range that starts
at or before the given position, proceeding backwards
through the genome, ordered by start position.
- reversePrefix - Property in RestrictionEnzyme
-
- reversePrefixPattern - Property in RestrictionEnzyme
-
- reverseSuffix - Property in RestrictionEnzyme
-
- reverseSuffixPattern - Property in RestrictionEnzyme
-
- root - Property in PrefixTrie
-
- run() - Method in AsyncMateResolveWorker
-
Main loop - runs forever
- run() - Method in CoveragePrinter
-
- run() - Method in DeletionPlot
-
- run() - Method in Delfin
-
- run() - Method in DownsampleFASTQ
-
- run() - Method in ExonCoverageStats
-
- run(java.io.Writer) - Method in ExtractFASTQ
-
- run() - Method in FastQIdent
-
- run() - Method in FindCompoundHets
-
- run() - Method in GeneCovStats
-
- run() - Method in Genotype
-
- run() - Method in HeaderCat
-
- run() - Method in LCSHPlot
-
- run() - Method in LiftOver
-
- run() - Method in MergePartitionedVCFs
-
- run(gngs.coverage.CoverageSummarizer, boolean) - Method in MultiCov
-
- run() - Method in Pairs
-
- run() - Method in RegulatingActor
-
- run() - Method in SampleCorrelationPlot
-
- run() - Method in Sex
-
- run() - Method in SexKaryotyper
-
The primary logic is simply that lack of coverage of the Y
chromosome indicates a female sample.
- run() - Method in ShearingKmerCounter
-
- run(java.io.Writer) - Method in SortFASTH10X
-
- run(int, int, java.io.Writer) - Method in SplitFASTQ10X
-
- run() - Method in SplitLiveFASTQ
-
- run() - Method in ToolBase
-
- run(java.io.Writer) - Method in TrimBarcode10X
-
- run() - Method in VariantInfo
-
- run() - Method in VCFtoDB
-
- run() - Method in VCFtoPed
-
- run(java.io.PrintWriter, java.lang.Object) - Method in VEPDiff
-
- running - Property in PairScanner
-
- SAM - Class in gngs
Adds various Groovy idioms and convenience features to the
Picard SamReader.
- SAM(java.io.File) - Constructor in SAM
-
- samFile - Property in SAM
-
- samFileReader - Property in SAM
-
- sample - Property in OrderedPairReader
-
- sample - Property in SampleInfo
-
Sample name
- sample - Property in SampleReadCount
-
- SampleCorrelationPlot - Class in gngs.tools
Computes pairwise SNP correlation for a set of input VCFs, outputting as a plot
or a table in TSV format.
- SampleCorrelationPlot() - Constructor in SampleCorrelationPlot
-
- SampleInfo - Class in gngs.sample
Meta data about a sample.
- SampleInfo() - Constructor in SampleInfo
-
- SampleReadCount - Class in gngs.coverage
The count of reads overlapping a base at a position for a sample
- SampleReadCount(gngs.Region, java.lang.String, int, int, java.lang.String) - Constructor in SampleReadCount
-
- samples - Property in SAM
-
List of samples in the BAM file.
- samples - Property in VCFSimilarity
-
- SamplesToPed - Class in SamplesToPed
- SamplesToPed() - Constructor in SamplesToPed
-
- samplesToVCF - Property in VCFtoPed
-
- SampleType - Enum in gngs.sample
- sampleType - Property in SampleInfo
-
Whether the sample type is normal or tumor
- sampleVariantMetrics - Property in VCFSimilarity
-
- SAMRecordCategory - Class in gngs
A convenience class to streamline working with SAMRecord objects
- SAMRecordCategory() - Constructor in SAMRecordCategory
-
- samStream - Property in SAM
-
Only used when created from stream
- samWriter - Property in OrderedPairWriter
-
- save(java.io.Writer) - Method in Pedigrees
-
- save(java.util.Map, java.io.Writer) - Method in Regions
-
Save the regions in BED format.
- saveJson(java.lang.String) - Method in DeletionPlot
-
- scan(gngs.SAM) - Method in PairScanner
-
- ScannableRegion - Class in gngs
- ScannableRegion() - Constructor in ScannableRegion
-
- scanRegions - Property in MultiCov
-
- scheduleAsyncResolves() - Method in OrderedPairReader
-
- scheduleTimeMs - Property in ResolveRequest
-
- Schema - Class in gngs.db
The default schema, which uses SQLite syntax
- schema - Property in Schema
-
- schema - Property in VariantDB
-
Schema for database
- schemaInfo - Property in Schema
-
Meta data about schema that this database is connected to
- score - Property in BaseCounts
-
- sdThreshold - Property in MeanCoverageEstimator
-
- searchForVariant(gngs.VCF, java.lang.String, java.lang.String) - Method in VariantInfo
-
- seedSize - Property in FASTAIndex
-
Size of seed to use (bp)
- send(gngs.AcknowledgeableMessage) - Method in RegulatingActor
-
- sendDownstream(java.lang.Object) - Method in RegulatingActor
-
- sendLimited(gngs.AcknowledgeableMessage, boolean) - Method in RegulatingActor
-
- sendStop() - Method in RegulatingActor
-
Send a pre-determined STOP message to the actor, which when receieved, will cause
it to call terminate().
- sendTo(T) - Method in RegulatingActor
-
- separator - Property in RangedData
-
The separator used between values in the file
- sequenceNames - Property in FASTAIndex
-
Index of amplicon names maps name => full sequence
- sequences - Property in FASTAIndex
-
Index of amplicon sequences, maps subsequence to amplicon name(s)
- sequencingContact - Property in SampleInfo
-
- sequencingDates - Property in SampleInfo
-
- setMinMappingQuality(int) - Method in PileupIterator
-
- setProxy() - Method in ToolBase
-
Check if the http_proxy variable is set, and if no proxy set, initialize the system properties
needed from there.
- severityOf(java.lang.String) - Method in VepConsequence
-
- severityOfConsequence(gngs.VepConsequence) - Method in VepConsequence
-
- Sex - Class in gngs.tools
Estimates the sex of a sample from one or more VCF file and prints to the console.
- sex - Property in SampleInfo
-
The sex of the sample
- Sex() - Constructor in Sex
-
- sex - Property in SexKaryotyper
-
- sex - Property in Subject
-
- SexKaryotyper - Class in gngs
An algorithm based on simple heuristics for estimating the sex of a sample from
sequencing coverage.
- SexKaryotyper.1 - Class in gngs
- SexKaryotyper.1() - Constructor in SexKaryotyper.1
-
- SexKaryotyper(gngs.SAM, gngs.Regions) - Constructor in SexKaryotyper
-
- sha1(java.lang.String, java.lang.String) - Method in Hash
-
- sha256(java.lang.String, java.lang.String) - Method in Hash
-
- shardId - Property in PairScanner
-
- shardSize - Property in PairScanner
-
- sharedCounts - Property in VCFSimilarity
-
- ShearingKmerCounter - Class in gngs.tools
Tool to count the frequency of kmers at the start
of each read in a BAM file.
- ShearingKmerCounter() - Constructor in ShearingKmerCounter
-
- shell - Property in PairFilter
-
- shuffleBufferSize - Property in PairScanner
-
The buffer within which to shuffle reads so as to randomise their output order
- shufflerPGroup - Property in PairScanner
-
- shufflers - Property in PairScanner
-
- shutdown() - Method in OrderedPairActor
-
- SIMPLE_COLUMNS - Property in SampleInfo
-
- SimpleLogFormatter - Class in gngs
The default Java log former uses a format that is too verbose, so
this class replaces it with something more compact.
- size() - Method in CoverageBlock
-
- size() - Method in FASTHRead
-
- size() - Method in OverlapTracker
-
- size() - Method in Regions
-
- size() - Method in SAM
-
Count the total number of reads in the SAM file
- smaller - Property in GnomADHist
-
- sniffGenomeBuild(Map<String, Integer>) - Method in GenomeInfo
-
Infers the identity of the genome build used based on given contig sizes.
- sniffGenomeBuild() - Method in SAM
-
Probe the given BAM file to make a guess about what genome build it is
generated from.
- SnpEffInfo - Class in gngs
Support for parsing annotations from SnpEff
- SnpEffInfo() - Constructor in SnpEffInfo
-
- snpName - Property in IlluminaSNPData
-
- soAccession - Property in VepConsequence
-
- SortFASTH10X - Class in gngs.tools
Utility to sort interleaved 10X FASTH format
- SortFASTH10X() - Constructor in SortFASTH10X
-
- source - Property in Gencode
-
- source - Property in RangedData
-
- spanning - Property in CNVFrequency
-
- spanningFreq - Property in CNVFrequency
-
- SPLICE_ACCEPTOR_VARIANT - Field in VepConsequence
-
- SPLICE_DONOR_VARIANT - Field in VepConsequence
-
- SPLICE_REGION_VARIANT - Field in VepConsequence
-
- SplitFASTQ10X - Class in gngs.tools
Utility to split paired end FASTQ and write it out in interleaved 10X format
- SplitFASTQ10X() - Constructor in SplitFASTQ10X
-
- SplitLiveFASTQ - Class in gngs.tools
Splits FASTQ in block-gzipped files which can be written live simultaneously
while this tool is streaming them out.
- SplitLiveFASTQ() - Constructor in SplitLiveFASTQ
-
- splitReadBinSize - Property in DeletionPlot
-
- spoolSize - Property in ExtractFASTQ
-
- spoolStats() - Method in OrderedPairReader
-
- start - Property in CoverageBlock
-
- START_LOST - Field in VepConsequence
-
- start - Field in Pileup
-
- start - Field in PileupIterator
-
- START_RETAINED_VARIANT - Field in VepConsequence
-
- startColumn - Property in BED
-
- startColumn - Property in RangedData
-
Index of the column containing the start index
- startingAt(int) - Method in RangeIndex
-
- startingAt(java.lang.String, int) - Method in Regions
-
- startsWith(java.lang.String, int, int, int, int) - Method in PrefixTrie
-
Return all values that match the given key, allowing for the specified number
of mismatches, insertions, deletions and leading optional bases.
- startsWith(java.lang.String, trie.TrieQuery, int) - Method in TrieNode
-
- startTimeMs - Property in ProgressCounter
-
- stats(gngs.Region) - Method in BEDToolsCoverage
-
- stats - Property in CoverageBlock
-
- stats - Property in CoverageDownsampler
-
- stats - Property in CoveragePosition
-
- statsMaxPctValue - Property in MultiCov
-
- STOP_GAINED - Field in VepConsequence
-
- STOP_LOST - Field in VepConsequence
-
- STOP - Property in RegulatingActor
-
- STOP_RETAINED_VARIANT - Field in VepConsequence
-
- stopActor(java.lang.String, groovyx.gpars.actor.Actor) - Method in PairScanner
-
- stopped - Property in OrderedPairActor
-
- stopped - Property in RegulatingActor
-
- strict - Property in IlluminaFileNameParser
-
Mainly to allow some simple tests to work, we can let parsing be less strict
In that case, the sample name may be determined purely as all characters up to the
first underscore.
- stripChr - Property in GenomeResource
-
- Subject - Class in gngs
An individual in a family pedigree
- Subject(gngs.Subject) - Constructor in Subject
-
- subjects - Property in Pedigrees
-
Look up table to find pedigree by subject Ids
- subsampleBy - Property in CoverageDownsampler
-
- subtract(gngs.Regions) - Method in Regions
-
- subtractFrom(int, int) - Method in RangeIndex
-
Subtract all the ranges in this range index from the given range and return
the resulting list of ranges.
- subtractFrom(java.lang.String, int, int) - Method in Regions
-
Remove all of the regions belonging to this
Regions object
from the interval specified, and return the list of Ranges that results.
- summarize(gngs.Variant) - Method in VInfo
-
- SUSPECTED - Field in Consanguinity
-
- SYNONYMOUS_VARIANT - Field in VepConsequence
-
- T - Field in BaseCompactor
-
- t - Property in BaseCounts
-
- TAB - Property in OMIM
-
- Table - Class in gngs.tools
- table(groovy.lang.Closure) - Method in PDF
-
- Table() - Constructor in Table
-
- tableBackground - Property in PDF
-
- tableOpts - Property in PDF
-
- target - Property in SampleInfo
-
Target (flagship) name
- target - Property in SampleReadCount
-
- target - Property in TargetedCNVAnnotator
-
- TargetedCNVAnnotator - Class in gngs
- TargetedCNVAnnotator(Map<String, CNVDatabase>, gngs.Regions) - Constructor in TargetedCNVAnnotator
-
- TargetedCoverageCalculator - Class in gngs.coverage
Optimised class to count reads over a given set of target regions
- TargetedCoverageCalculator(gngs.SAM, gngs.Regions) - Constructor in TargetedCoverageCalculator
-
- targetRegionGCRfractions - Property in Delfin
-
- targetRegions - Property in GeneCovStats
-
- targets - Property in Delfin
-
- term - Property in VepConsequence
-
- test(gngs.Variant, List<Pedigree>) - Method in Constraint
-
- test - Property in ToolBase
-
- testCall() - Method in LiftOver
-
- TestUpdate - Class in TestUpdate
- TestUpdate() - Constructor in TestUpdate
-
- TF_BINDING_SITE_VARIANT - Field in VepConsequence
-
- TFBS_ABLATION - Field in VepConsequence
-
- TFBS_AMPLIFICATION - Field in VepConsequence
-
- theta - Property in IlluminaSNPData
-
- thin(int, int) - Method in Regions
-
Select the given number of ranges from these, approximately evenly spaced
- thinnedIndices(int, int) - Method in Regions
-
The same as
thin(int,int) but returns the indices of the
regions to keep.
- THREE_PRIME_UTR_VARIANT - Field in VepConsequence
-
- threshold - Property in CoverageGaps
-
- throttled - Property in RegulatingActor
-
- throttleWarning - Property in PairScanner
-
- throttleWarningMs - Property in RegulatingActor
-
- Time - Class in Time
- Time() - Constructor in Time
-
- timeInterval - Property in ProgressCounter
-
- timings - Property in Time
-
- title(java.lang.Object) - Method in PDF
-
- to - Property in LiftOver
-
- toAlignment(java.lang.String) - Method in PDF
-
- toColor(java.lang.String) - Method in PDF
-
- toHTML() - Method in Regions
-
- toJson() - Method in Pedigrees
-
- toJson() - Method in Subject
-
- toListMap() - Method in RangedData
-
Convert to a list of map objects
- toListMap() - Method in Regions
-
A convenience method to return the contained regions as a list of Map objects.
- toMap() - Method in VepConsequence
-
- ToolBase - Class in gngs
A support class that makes implementing a tool based on GNGS very easy
while supporting some standard behaviors (such as logging, etc).
- Toolbase9 - Class in gngs.tools
- ToolBase() - Constructor in ToolBase
-
- toPairRegions(java.lang.String, int, int, int) - Method in SAM
-
Return read pairs from this SAM file that overlap the specified region
as a Regions object - that is, as a set of genomic intervals.
- toQueryIntervals(gngs.Regions) - Method in SAM
-
- toRegex(java.lang.String) - Method in RestrictionEnzyme
-
Convert N's to wildcards and select IUPAC codes to appropriate character sets
- toRegion(htsjdk.samtools.BAMRecord) - Method in SAMRecordCategory
-
- toRegions(java.lang.String, int, int) - Method in SAM
-
Return reads from this SAM file that overlap the specified region
as a Regions object - that is, as a set of genomic intervals.
- toString() - Method in BaseCounts
-
- toString() - Method in BED
-
- toString() - Method in Feature
-
- toString() - Method in ReadRange
-
- toString() - Method in ReadSpans
-
- toString() - Method in ReadWindow
-
- toString() - Method in Regions
-
- toString() - Method in RestrictionEnzyme
-
- toString() - Method in SampleInfo
-
- toString() - Method in SnpEffInfo
-
- toString() - Method in Subject
-
- toString() - Method in VCFSummaryStats
-
- toString() - Method in XA
-
- total - Property in FASTQDedupeActor
-
- total - Property in ProgressCounter
-
Optional total: if provided, percentage progress can be displayed
- total - Property in VariantInjector
-
- total - Property in VCFSummaryStats
-
- totalBP - Property in CoverageGaps
-
- totalIncluded - Property in VCFSummaryStats
-
- toTsv(List<String>, java.lang.String, java.lang.String) - Method in SampleInfo
-
Return a tab separated string compatible with the samples.txt file format,
containing the details for this sample.
- TRANSCRIPT_ABLATION - Field in VepConsequence
-
- TRANSCRIPT_AMPLIFICATION - Field in VepConsequence
-
- transcript - Property in SnpEffInfo
-
The transcript impacted (if any) by the variant
- transcriptIndex - Property in RefGenes
-
- translation - Property in ShearingKmerCounter
-
- TrieMismatchCosts - Class in trie
- TrieMismatchCosts() - Constructor in TrieMismatchCosts
-
- TrieNode - Class in trie
- TrieNode() - Constructor in TrieNode
-
- TrimBarcode10X - Class in gngs.tools
Utility to filter 10X barcode off the R1 FASTQ
- TrimBarcode10X() - Constructor in TrimBarcode10X
-
- trimSampleId(java.lang.String) - Method in VariantDB
-
- TSV - Class in TSV
This class is just an alias to bring the Graxxia TSV class
into the default namespace.
- TSV(java.lang.String) - Constructor in TSV
-
- TUMOR - Field in SampleType
-
- TwoLeggedOAuthAPI - Class in gngs
With 2 legged OAuth there is no need for acquiring an access token or request token; these
are presumed known.
- TwoLeggedOAuthAPI() - Constructor in TwoLeggedOAuthAPI
-
- tx(groovy.lang.Closure) - Method in VariantDB
-
Execute the given closure in teh scope of a transaction, and roll it back if
an exception occurs.
- type - Property in CustomInfo
-
- type - Property in FormatMetaData
-
- type - Property in SnpEffInfo
-
The kind of impact.
- type - Property in VepConsequence
-