Index (MUSIAL v2.4.2 API)

A B C D E F G H I L M N O P Q R S T U V W _
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

active - Variable in class model.Variant: Indicates whether this variant is active.
addAllele(Allele) - Method in class model.Feature: Adds an allele to this feature.
addAlleleRelation(String, String) - Method in class model.Variant: Associates an allele and its parent feature with this variant.
addContig(String, String) - Method in class model.Storage: Adds a contig to the storage under the specified id and sequence.
addContigFilter(String, int[]) - Method in class op.StorageTable: Updates the contig filter with the specified contig identifier and positions.
addFeature(String, String, Number, Number, char, String, Map<String, String>) - Method in class model.Storage: Adds feature information to the storage.
addFeature(FeatureI, String, Map<String, String>) - Method in class model.Storage: Adds feature information from a FeatureI object to the storage.
addFeatureFilter(String) - Method in class op.StorageTable: Adds a feature filter using the provided identifier or name.
addProteoform(Proteoform) - Method in class model.Feature: Adds a proteoform to this feature.
addRelation(String) - Method in class model.Proteoform: Associates an allele with this proteoform.
addRelation(String, String) - Method in class model.Sample: Associates a specific allele of a feature with this sample.
addSample(String) - Method in class model.Storage: Adds a sample to the storage if it does not already exist.
addSampleFilter(String) - Method in class op.StorageTable: Adds a sample filter using the provided identifier.
addSampleRelation(String) - Method in class model.Allele: Associates a sample with this allele.
addSampleRelation(String, Set<VariantCall>) - Method in class model.Variant: Associates a sample with this variant by adding the sample identifier and its associated variant calls.
addSubFeature(String, int, int) - Method in class model.Feature: Adds a sub-feature to this genomic feature.
addVariant(Contig, String, int, String, String, Set<VariantCall>) - Method in class model.Storage: Adds a variant to the specified contig in the storage.
align - Variable in class cli.CLISequence: Indicates whether to align sequences.
alignByCigar(String, String, String, int) - Static method in class util.Bio: Aligns a query sequence to a reference sequence based on a CIGAR string.
Allele - Class in model: Represents an allele, which is a specific sequence type associated with a set of samples and a proteoform.
Allele(List<Variant.Stub>) - Constructor for class model.Allele: Constructs an Allele instance with the specified variants.
ALLELES - Enum constant in enum class cli.CLIProfile.Content: Per sample alleles.
ALLELIC_FREQUENCY - Static variable in class util.Constants.AttributesKeys: Key representing the frequency of a SequenceType with respect to Samples.
alternative - Variable in class model.Variant: The alternative base content of this variant.
alternative() - Method in record class model.Variant.Stub: Returns the value of the alternative record component.
alternative() - Method in record class model.VariantCall.CallAlternative: Returns the value of the alternative record component.
alternatives() - Method in record class model.VariantCall: Returns the value of the alternatives record component.
AMINOACID - Enum constant in enum class cli.CLISequence.Content: Protein sequences.
AminoacidSequenceGenerator - Class in op: The AminoacidSequenceGenerator class is responsible for generating aminoacid sequences based on genomic data contained in a Storage instance.
AminoacidSequenceGenerator(Storage, Contig, Feature, boolean, boolean, Set<String>) - Constructor for class op.AminoacidSequenceGenerator: Constructs a new instance of the AminoacidSequenceGenerator class.
ANY_NUCLEOTIDE - Static variable in class util.Constants: IUPAC symbol for any/unknown nucleotide in a nucleotide sequence.
asMaskedStub() - Method in class model.Variant: Converts this variant to a masked stub representation.
asStub() - Method in class model.Variant: Converts this variant to a simplified stub representation.
Attributes - Class in model: Base class for entities to store arbitrary attributes as Strings.
attributesAsString(String) - Method in class model.Attributes: Converts the attributes of this entity to a string representation..
attributesAsString(Collection<String>, String) - Method in class model.Attributes: Converts the attributes of this entity to a string representation, excluding attributes with keys in the specified collection.
AttributesKeys() - Constructor for class util.Constants.AttributesKeys

B

BASE_SYMBOLS - Static variable in class util.Constants: Base symbols of the IUPAC nucleotide and amino acid code.
Bio - Class in util: Utility class for performing various sequence related operations.
Bio.ReferenceContext - Record Class in util: Represents information about a single position in a reference sequence.
BOTH - Enum constant in enum class cli.CLISequence.Split: Split output files by both feature/genomic range and sample (or sequence type) identifier.
BUILD - Enum constant in enum class main.MusialTask: Task to build a MUSIAL storage file.

C

cache - Static variable in class util.Logging: Set to keep track of logged warnings to avoid duplicate messages.
CallAlternative(String, String, short) - Constructor for record class model.VariantCall.CallAlternative: Creates an instance of a CallAlternative record class.
character() - Method in record class util.Bio.ReferenceContext: Returns the value of the character record component.
clearAttributes() - Method in class model.Attributes: Removes all attributes from this entity.
clearFilters() - Method in class op.StorageTable: Clears all filters used for building the table.
clearSubFeatures() - Method in class model.Feature: Clears all sub-features associated with this genomic feature.
clearSubFeatures(int) - Method in class model.Feature: Clears all sub-features of a specific Sequence Ontology (SO) hierarchy level associated with this genomic feature.
cli - package cli: Encapsulates management of command line argument parsing and validation for each MusialTask.
CLI - Interface in cli: Interface representing a Command Line Interface (CLI) component.
CLIBuild - Class in cli: Handles the build task CLI parameters.
CLIBuild(CommandLine) - Constructor for class cli.CLIBuild: Constructs a CLIBuild instance by parsing and initializing configuration parameters.
CLIExpand - Class in cli: Handles the expand task CLI parameters.
CLIExpand(CommandLine) - Constructor for class cli.CLIExpand: Constructs a CLIExpand instance by parsing and initializing the command-line arguments.
CLIProfile - Class in cli: Handles the profile task CLI parameters.
CLIProfile(CommandLine) - Constructor for class cli.CLIProfile: Constructs a CLIView instance by parsing the provided command-line arguments.
CLIProfile.Content - Enum Class in cli: The content type to profile.
CLISequence - Class in cli: Handles the sequence task CLI parameters.
CLISequence(CommandLine) - Constructor for class cli.CLISequence: Constructs a new CLISequence instance and initializes its fields based on the provided command-line arguments.
CLISequence.Content - Enum Class in cli: The content type to generate sequences of.
CLISequence.Split - Enum Class in cli: The mode to split output files by.
CLIView - Class in cli: Handles the view task CLI parameters.
CLIView(CommandLine) - Constructor for class cli.CLIView: Constructs a CLIView instance by parsing the provided command-line arguments.
CLIView.Content - Enum Class in cli: The content type to view.
close() - Method in class op.VCFProcessor
COLON - Static variable in class util.Constants: Colon string constant.
COMMA - Static variable in class util.Constants: Comma string constant.
Constants - Class in util: Utility class that holds constant values used throughout the application.
Constants() - Constructor for class util.Constants
Constants.AttributesKeys - Class in util: A nested utility class that defines keys for various attributes used in the application.
contact - Static variable in class main.Musial: Author contact of the software; parsed from `/src/main/resources/info.properties`.
content - Variable in class cli.CLIProfile: The content type specified by the user.
content - Variable in class cli.CLISequence: The content type specified by the user.
content - Variable in class cli.CLIView: The content type specified by the user.
contig - Variable in class model.Feature: The parent genomic location of this feature.
Contig - Class in model: Represents a reference genomic location.
contigIdentifier() - Method in record class op.VCFProcessor.UpstreamDeletion: Returns the value of the contigIdentifier record component.
copyResourceToFile(String, Path) - Static method in class util.IO: Copies a resource from the application's classpath to a specified target Path.

D

DELETION - Enum constant in enum class model.Variant.Type: A deletion of one or more nucleotides
depth() - Method in record class model.VariantCall.CallAlternative: Returns the value of the depth record component.
depth() - Method in record class model.VariantCall: Returns the value of the depth record component.
detachSample(String) - Method in class model.Storage: Detaches a sample from the storage and removes its associations with variants and alleles.
DIVERSITY_ALLELE - Static variable in class util.Constants.AttributesKeys: Key representing the diversity of alleles associated with a Feature.
DIVERSITY_PROTEOFORM - Static variable in class util.Constants.AttributesKeys: Key representing the diversity of proteoforms associated with a Feature.
DOT - Static variable in class util.Constants: Dot string constant.
dry - Variable in class cli.CLIExpand: Indicates whether dry-run mode is enabled.

E

EMPTY - Static variable in class util.Constants: Empty string constant.
end - Variable in class model.Feature: 1-based end position of the feature.
end() - Method in record class model.Feature.SubFeature: Returns the value of the end record component.
end() - Method in record class op.VCFProcessor.UpstreamDeletion: Returns the value of the end record component.
entropy() - Method in record class model.VariantCall: Returns the value of the entropy record component.
EQUAL - Static variable in class util.Constants: Equals sign string constant.
equals(Object) - Method in class model.Allele: Compares this allele to another object for equality.
equals(Object) - Method in class model.Contig: Compares this contig to another object for equality.
equals(Object) - Method in class model.Feature: Compares this feature to another object for equality.
equals(Object) - Method in record class model.Feature.SubFeature: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class model.Proteoform: Compares this proteoform to another object for equality.
equals(Object) - Method in class model.Sample: Compares this sample to another object for equality.
equals(Object) - Method in record class model.Storage.Parameters: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class model.Variant: Compares this variant to another object for equality.
equals(Object) - Method in record class model.Variant.Stub: Compares this variant stub to another object for equality.
equals(Object) - Method in record class model.VariantCall.CallAlternative: Compares this alternative allele to another object for equality.
equals(Object) - Method in record class model.VariantCall: Compares this variant call to another object for equality.
equals(Object) - Method in record class op.VCFProcessor.UpstreamDeletion: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class util.Bio.ReferenceContext: Indicates whether some other object is "equal to" this one.
equals(VariantCall, ByteBuffer) - Method in class model.VariantCall.VariantCallSerializer: Compares a VariantCall object with its binary representation for equality.
exceptions - package exceptions: Defines application-specific exceptions to handle internal error scenarios.
ExecutorBuild - Class in task: The ExecutorBuild class is responsible for executing the build task to compile genomic data.
ExecutorBuild(CLIBuild) - Constructor for class task.ExecutorBuild: Constructs an instance of the ExecutorBuild class.
ExecutorExpand - Class in task: The ExecutorExpand class is responsible for executing the expand task to extend existing genomic data.
ExecutorExpand(CLIExpand) - Constructor for class task.ExecutorExpand: Constructs an instance of the ExecutorExpand class.
ExecutorProfile - Class in task: The ExecutorProfile class is responsible for executing the profile task to profile samples.
ExecutorProfile(CLIProfile) - Constructor for class task.ExecutorProfile: Constructs an instance of the ExecutorProfile class.
ExecutorSequence - Class in task: The ExecutorSequence class is responsible for executing the sequence task to profile samples.
ExecutorSequence(CLISequence) - Constructor for class task.ExecutorSequence: Constructs an ExecutorSequence instance with the specified command-line interface.
ExecutorView - Class in task: The ExecutorView class is responsible for executing the view task for inspecting data.
ExecutorView(CLIView) - Constructor for class task.ExecutorView: Constructs an instance of the ExecutorView class.
EXPAND - Enum constant in enum class main.MusialTask: Task to add (sample) data from VCF files to a MUSIAL storage file.
extendAttribute(String, String) - Method in class model.Attributes: Extends an attribute by appending a value to the existing value.
extendAttributes(Map<String, String>) - Method in class model.Attributes: Extends multiple attributes by appending values to the existing values.
extension() - Method in record class util.Bio.ReferenceContext: Returns the value of the extension record component.

F

Feature - Class in model: Representation of a genomic feature.
Feature(String, String, Number, Number, char, String, String) - Constructor for class model.Feature: Constructs a new Feature instance with the specified properties.
FEATURE - Enum constant in enum class cli.CLISequence.Split: Split output files by feature/genomic range.
Feature.SubFeature - Record Class in model: Represents a sub-feature of a genomic feature.
featureList - Variable in class cli.CLIBuild: The list of features parsed from the annotation file.
FeatureLoader - Class in op: The FeatureLoader class is responsible for loading and validating genomic features.
FeatureLoader(Storage, FeatureList, Map<String, Map<String, String>>) - Constructor for class op.FeatureLoader: Constructs a new instance of the FeatureLoader class.
features - Variable in class cli.CLIBuild: A map containing the features to be matched, with the feature ID as the key and another map of at least a `key` and `value` attribute to match the feature with.
FEATURES - Enum constant in enum class cli.CLIView.Content: The features of the storage.
flag() - Method in record class model.VariantCall: Returns the value of the flag record component.
formatFrequency(double) - Static method in class util.IO: Formats a frequency value into scientific notation.
formatNumber(double) - Static method in class util.IO: Formats a number to three decimal places.
FREQUENCY_DISRUPTED - Static variable in class util.Constants.AttributesKeys: Key representing the fraction of disrupted proteoforms with respect to a Sample or Feature.
FREQUENCY_FILTERED_CALLS - Static variable in class util.Constants.AttributesKeys: Key representing the fraction of filtered calls in a Sample.
FREQUENCY_REFERENCE - Static variable in class util.Constants.AttributesKeys: Key representing the fraction of reference alleles with respect to a Sample or Feature.
fromCli(CLIBuild) - Static method in class op.StorageFactory: Constructs a Storage object from definitions in CLIBuild.
fromPath(Path) - Static method in class op.StorageFactory: Reads a Storage object from the specified file path.
fromString(String) - Static method in record class model.VariantCall: Creates a VariantCall object from its string representation.

G

GAP - Static variable in class util.Constants: String representation of a gap in a sequence.
GAP_CHAR - Static variable in class util.Constants: Character representation of a gap in a sequence.
generateConservedContext() - Method in class op.AminoacidSequenceGenerator: Generates the conserved nucleotide context for the sequence generator.
generateContext() - Method in class op.AminoacidSequenceGenerator: Generates the amino acid context for the sequence generator.
GENOMIC_COORDINATES_PREFIX - Static variable in class util.Constants: Prefix for genomic coordinate notation as per HGVS guidelines.
getActiveSamples() - Method in class model.Storage: Retrieves a collection of active samples from the storage.
getActiveVariants() - Method in class model.Contig: Retrieves all active variants associated with this contig.
getActiveVariantsCount() - Method in class model.Contig: Calculates the total number of active variants associated with this contig.
getActiveVariantsCount() - Method in class model.Storage: Calculates the total number of active variants across all contigs in the storage.
getAllele(String) - Method in class model.Feature: Retrieves an allele associated with this feature by its unique identifier (_id) or null.
getAlleleCount() - Method in class model.Feature: Retrieves the number of alleles associated with this feature.
getAlleles() - Method in class model.Feature: Retrieves all alleles associated with this feature.
getAllVariants() - Method in class model.Contig: Retrieves all variants associated with this contig.
getAlternative() - Method in record class model.VariantCall: Retrieves the alternative content of the first (called) alternative of this variant call.
getAlternative(int) - Method in record class model.VariantCall: Retrieves the alternative content of the i-th alternative of this variant call.
getAttribute(String) - Method in class model.Attributes: Retrieves the value of an attribute associated with this entity.
getAttributeOrDefault(String, String) - Method in class model.Attributes: Retrieves the value of an attribute associated with this entity.
getAttributes() - Method in class model.Attributes: Retrieves all attributes associated with this entity.
getAttributeSet(String) - Method in class model.Attributes: Retrieves the value of an attribute as a collection of strings.
getCanonicalVariants(String, String) - Static method in class util.Bio: Transforms two sequences into canonical VCF variants.
getContig(String) - Method in class model.Storage: Retrieves a contig by its unique identifier.
getContigs() - Method in class model.Storage: Retrieves an unmodifiable collection view of the contigs stored in the storage.
getDate() - Static method in class util.Logging: Returns the current date formatted as a string.
getFeature(String) - Method in class model.Storage: Retrieves a feature from the storage by its unique identifier.
getFeatureAttributeKeys() - Method in class model.Storage: Retrieves the set of all unique attribute keys from features in the storage.
getFeatureRelation(String) - Method in class model.Variant: Retrieves a set of allele identifiers associated with a specific feature for this variant.
getFeatures() - Method in class model.Storage: Retrieves an unmodifiable collection view of the features stored in the storage.
getFilteredCallsCount() - Method in class op.VCFProcessor: Retrieves the total number of filtered variant calls.
getIgnoredCallsCount() - Method in class op.VCFProcessor: Retrieves the total number of ignored variant calls.
getLoadedFeatureCount() - Method in class op.FeatureLoader: Retrieves the total number of features successfully processed, including sub-features.
getName(boolean) - Method in class op.NucleotideSequenceGenerator: Retrieves the name of the sequence generator.
getName(boolean) - Method in interface op.SequenceGenerator: Retrieves the name of the sequence generator.
getProcessedCallsCount() - Method in class op.VCFProcessor: Retrieves the total number of processed variant calls.
getProteoform(String) - Method in class model.Feature: Retrieves a proteoform associated with this feature by its unique identifier or null.
getProteoformCount() - Method in class model.Feature: Retrieves the number of proteoforms associated with this feature.
getProteoforms() - Method in class model.Feature: Retrieves all proteoforms associated with this feature.
getRealignedCallsCount() - Method in class op.VCFProcessor: Retrieves the total number of realigned variant calls.
getReference() - Method in record class model.VariantCall: Retrieves the reference content of the first (called) alternative of this variant call.
getReference(int) - Method in record class model.VariantCall: Retrieves the reference content of the i-th alternative of this variant call.
getRelatedAllele(String) - Method in class model.Sample: Retrieves the allele associated with a specific feature in this sample.
getRelatedAlleles() - Method in class model.Proteoform: Retrieves a collection of allele identifiers associated with this proteoform.
getRelatedAlleles() - Method in class model.Sample: Retrieves all feature-allele associations in this sample.
getRelatedAlleles() - Method in class model.Variant: Retrieves a set of tuples representing the feature and allele occurrences associated with this variant.
getRelatedAllelesCount() - Method in class model.Sample: Retrieves the number of alternate alleles in this sample.
getRelatedProteoform() - Method in class model.Allele: Retrieves the proteoform identifier associated with this allele.
getRelatedSamples() - Method in class model.Allele: Retrieves a collection of sample identifiers associated with this allele.
getRelatedSamples() - Method in class model.Variant: Retrieves a set of sample identifiers that have occurrences of this variant.
getRelatedSamplesCount() - Method in class model.Allele: Retrieves the number of unique samples associated with this allele.
getSample(String) - Method in class model.Storage: Retrieves a sample from the storage by its unique identifier.
getSampleAttributeKeys() - Method in class model.Storage: Retrieves the set of all unique attribute keys from samples in the storage.
getSampleRelation(String) - Method in class model.Variant: Retrieves the variant call string associated with a specific sample.
getSamples() - Method in class model.Storage: Retrieves an unmodifiable collection view of the samples stored in the storage.
getSamples() - Method in class op.VCFProcessor: Retrieves an unmodifiable collection of sample identifiers.
getSequence() - Method in class model.Contig: Retrieves the full nucleotide sequence of this contig or an empty string if no sequence is stored.
getSequence(int, int) - Method in class model.Contig: Retrieves a subsequence of this contig, caching the result to optimize performance.
getSequence(String) - Method in class op.AminoacidSequenceGenerator: Retrieves the amino acid sequence for a given sample identifier.
getSequence(String) - Method in class op.NucleotideSequenceGenerator: Retrieves the nucleotide sequence for a given sample identifier.
getSequence(String) - Method in interface op.SequenceGenerator: Generates a sequence based on the provided sample identifier.
getSequenceLength() - Method in class model.Contig: Retrieves the length of the contig's sequence.
getStubs() - Method in class model.SequenceType: Retrieves all variants as stubs.
getSubFeatures() - Method in class model.Feature: Retrieves all sub-features associated with this genomic feature.
getTimestamp() - Static method in class util.Logging: Returns the current timestamp formatted as a string.
getVariant(int) - Method in class model.SequenceType: Retrieves the alternative allele at the specified position.
getVariant(int, String) - Method in class model.Contig: Retrieves a variant associated with the specified position and alternative base sequence.
getVariants() - Method in class model.SequenceType: Retrieves an unmodifiable view of the variants map.
getVariantsAt(int...) - Method in class model.Contig: Retrieves variants at the specified positions.
getVariantsCount() - Method in class model.Contig: Calculates the total number of variants associated with this contig.
getVariantsCount() - Method in class model.Storage: Calculates the total number of variants across all contigs in the storage.
getVariantsOfSamples(Collection<String>) - Method in class model.Contig: Retrieves variants associated with the specified sample identifiers.
getVariantsOfSamplesWithin(int, int, Collection<String>) - Method in class model.Contig: Retrieves variants associated with the specified sample identifiers within a given range of positions.
getVariantsWithin(int, int) - Method in class model.Contig: Retrieves variants within the specified range of positions.
globalNucleotideSequenceAlignment(String, String, int, int, boolean, boolean, int) - Static method in class util.Bio: Computes optimal pairwise global nucleotide sequence alignment using a gap-affine (Gotoh) banded Needleman-Wunsch algorithm.
globalProteinSequenceAlignment(String, String, int, int, boolean, boolean, int) - Static method in class util.Bio: Computes optimal pairwise global amino acid sequence alignment using a gap-affine (Gotoh) banded Needleman-Wunsch algorithm.
GREATER_THAN - Static variable in class util.Constants: Greater than sign string constant.
gzipCompress(String) - Static method in class util.IO: Compresses a string using GZIP compression and encodes the result in Base64.
gzipDecompress(String) - Static method in class util.IO: Decompresses a Base64-encoded GZIP-compressed string.

H

hasAllele(String) - Method in class model.Feature: Checks if an allele with the specified identifier exists in this feature.
hasAnyAttribute() - Method in class model.Attributes: Checks if this entity has any attribute.
hasAttribute(String) - Method in class model.Attributes: Checks if an attribute with the specified key exists in this entity.
hasContig(String) - Method in class model.Storage: Checks if a contig is present in the storage by its unique identifier.
hasFeature(String) - Method in class model.Storage: Query whether a feature is stored in this instance by its id.
hashCode() - Method in class model.Allele: Computes the hash code for this allele.
hashCode() - Method in class model.Contig: Computes the hash code for this contig.
hashCode() - Method in class model.Feature: Computes the hash code for this feature.
hashCode() - Method in record class model.Feature.SubFeature: Returns a hash code value for this object.
hashCode() - Method in class model.Proteoform: Computes the hash code for this proteoform.
hashCode() - Method in class model.Sample: Computes the hash code for this sample.
hashCode() - Method in record class model.Storage.Parameters: Returns a hash code value for this object.
hashCode() - Method in class model.Variant: Computes the hash code for this variant.
hashCode() - Method in record class model.Variant.Stub: Computes the hash code for this variant stub.
hashCode() - Method in record class model.VariantCall.CallAlternative: Computes the hash code for this alternative allele.
hashCode() - Method in record class model.VariantCall: Computes the hash code for this variant call.
hashCode() - Method in record class op.VCFProcessor.UpstreamDeletion: Returns a hash code value for this object.
hashCode() - Method in record class util.Bio.ReferenceContext: Returns a hash code value for this object.
hasProteoform(String) - Method in class model.Feature: Checks if a proteoform with the specified identifier exists in this feature.
hasReference() - Method in class model.Storage: Checks if the reference sequence is set for the storage.
hasRelation(String) - Method in class model.Allele: Checks if this allele is associated with a specific sample by its identifier.
hasRelation(String) - Method in class model.Proteoform: Checks if this proteoform is associated with a specific allele by its identifier.
hasSample(String) - Method in class model.Storage: Checks if a sample is present in the storage by its unique identifier.
hasSequence() - Method in class model.Contig: Checks if this contig has an associated nucleotide sequence.
hasVariant(int, String) - Method in class model.SequenceType: Checks if a specific variant exists at the given position.
hasVariantAt(int) - Method in class model.SequenceType: Checks if this sequence type has a variant at the specified position.

I

ID(String) - Method in record class model.Feature.SubFeature: Generates a GFF3 conform identifier (ID) for a sub-feature based on its type and a parent identifier.
init(Level) - Static method in class util.Logging: Initializes the logging system with a specified logging level.
input - Variable in class cli.CLIExpand: The path to the input storage file.
input - Variable in class cli.CLIProfile: The path to the input storage file.
input - Variable in class cli.CLISequence: The path to the input storage file.
input - Variable in class cli.CLIView: The path to the input storage file.
INSERTION - Enum constant in enum class model.Variant.Type: An insertion of one or more nucleotides
integrateVariants(String, NavigableMap<Integer, String>, boolean) - Static method in class util.Bio: Integrates variants into a reference sequence.
integrateVariants(NavigableMap<Integer, Bio.ReferenceContext>, Map<Integer, String>, boolean) - Static method in class util.Bio: Integrates variants into a reference sequence.
IO - Class in util: Utility class for I/O related operations.
isCanonical(String, String) - Static method in class util.Bio: Determines whether a variant is canonical.
isCoding() - Method in class model.Feature: Determines if this feature is a coding feature.
isDeletion(String) - Static method in class util.Bio: Determines whether a variant is a deletion based on its alternative content.
isDeletion(String, String, boolean) - Static method in class util.Bio: Determines whether a variant is a deletion, i.e., either the reference base content is a string of any length of Constants.BASE_SYMBOLS and the alternative base content is a single base of Constants.BASE_SYMBOLS followed by Constants.GAPs matching the reference content's length (padded canonical), or the reference base content is a string of any length of Constants.BASE_SYMBOLS and the alternative content is a single base of Constants.BASE_SYMBOLS (un-padded canonical).
isDisrupted() - Method in class model.Proteoform: Determines if the proteoform is disrupted based on its sequence ontology (SO) effects.
isFiltered() - Method in class model.Variant: Checks if all variant calls for this variant are filtered.
isFiltered() - Method in record class model.VariantCall: Checks if the variant call is filtered.
isFiltered() - Method in record class op.VCFProcessor.UpstreamDeletion: Returns the value of the isFiltered record component.
isFiltered(String) - Method in class model.Variant: Checks if the variant is filtered with respect to a specific sample.
isFiltered(String) - Static method in record class model.VariantCall: Checks if a variant call string contains any filtered flags.
isFiltered(Collection<String>) - Method in class model.Variant: Checks if the variant is filtered with respect to all specified samples.
isInsertion(String) - Static method in class util.Bio: Determines whether a variant is an insertion based on its alternative content.
isInsertion(String, String, boolean) - Static method in class util.Bio: Determines whether a variant is an insertion, i.e., either the alternative base content is a string of any length of Constants.BASE_SYMBOLS and the reference base content is a single base of Constants.BASE_SYMBOLS followed by Constants.GAPs matching the alternative content's length (padded canonical), or the reference base content is a single base of Constants.BASE_SYMBOLS and the alternative content is a string of any length of Constants.BASE_SYMBOLS (un-padded canonical).
isPaddedCanonical(String, String) - Static method in class util.Bio: Determines whether a variant is padded canonical.
isPositionMasked(String, int) - Method in record class model.Storage.Parameters: Whether position is excluded on contig.
isReverse() - Method in class model.Feature: Returns if this feature is on the reverse strand.
isSubstitution(String) - Static method in class util.Bio: Determines whether a given alternative base content represents a substitution.
isSubstitution(String, String) - Static method in class util.Bio: Determines whether a variant is a substitution; i.e., both the reference and alternative base content match a single base of Constants.BASE_SYMBOLS.

L

license - Static variable in class main.Musial: License information of the software; parsed from `/src/main/resources/info.properties`.
LINE_SEPARATOR - Static variable in class util.Constants: System-dependent line separator string.
loadFeatures() - Method in class op.FeatureLoader: Loads features into the storage based on the provided annotations and specifications.
loadVariantCallsFromStorage() - Method in class op.VCFProcessor: Loads variant calls from the storage and processes them.
loci - Variable in class cli.CLISequence: The set of loci (features or genomic ranges) provided by the user.
logConfig(String) - Static method in class util.Logging: Logs a configuration message to the console with a timestamp.
logDebug(String) - Static method in class util.Logging: Logs an error message to the console with a timestamp.
logDone(String) - Static method in class util.Logging: Logs a message indicating completion with a timestamp.
logExit(String) - Static method in class util.Logging: Logs a critical exit message to the console with a timestamp.
logger - Static variable in class util.Logging: Logger instance for the application.
Logging - Class in util: Logging utility class for printing messages to the console with different severity levels.
logInfo(String) - Static method in class util.Logging: Logs an informational message to the console with a timestamp.
logSevere(String) - Static method in class util.Logging: Logs an error message to the console with a timestamp.
logWarning(String) - Static method in class util.Logging: Logs a warning message to the console with a timestamp.
logWarningOnce(String, String) - Static method in class util.Logging: Logs a warning message to the console with a timestamp, but only once for each unique key.
LOW_COVERAGE - Enum constant in enum class model.VariantCall.Flag: Indicates that the variant call has a coverage below the minimum threshold.
LOW_FREQUENCY - Enum constant in enum class model.VariantCall.Flag: Indicates that the variant call has a frequency below the minimum threshold.

M

main - package main: Core classes and entry point for the application.
main(String[]) - Static method in class main.Musial: The main entry point of the MUSIAL application.
masked() - Method in record class model.Storage.Parameters: Returns the value of the masked record component.
maskedPositions - Variable in class cli.CLIBuild: A map containing the masked positions, with the contig ID as the key and a set of excluded positions as the value.
maskFiltered - Variable in class cli.CLIBuild: If filtered variants should be treated as missing data (masked) or ignored.
maskFiltered() - Method in record class model.Storage.Parameters: Returns the value of the maskFiltered record component.
md5Hash(String) - Static method in class util.IO: Generates the MD5 hash of the given string.
MEAN_COVERAGE - Static variable in class util.Constants.AttributesKeys: Key representing the mean coverage of a Sample over all of its calls.
MEAN_ENTROPY - Static variable in class util.Constants.AttributesKeys: Key representing the mean entropy of a Sample over all of its calls.
merge - Variable in class cli.CLISequence: Indicates whether to merge identical sequences.
minimalCoverage - Variable in class cli.CLIBuild: The minimal depth of coverage wrt.
minimalCoverage() - Method in record class model.Storage.Parameters: Returns the value of the minimalCoverage record component.
minimalFrequency - Variable in class cli.CLIBuild: The minimal frequency wrt.
minimalFrequency() - Method in record class model.Storage.Parameters: Returns the value of the minimalFrequency record component.
MISSING_UPSTREAM_DELETION - Enum constant in enum class model.VariantCall.Flag: Indicates that the variant call is declared missing due to an upstream deletion, but the upstream deletion is not present or was filtered.
model - package model: Constitutes the storage model of the MUSIAL application.
Musial - Class in main: Main class of MUSIAL (MUlti Sample varIant AnaLysis).
MusialException - Exception Class in exceptions: A custom exception class for handling application-specific errors.
MusialException(String) - Constructor for exception class exceptions.MusialException: Constructs a new MusialException with the specified detail message.
MusialTask - Enum Class in main: Enum specifying MUSIAL tasks.

N

name - Static variable in class main.Musial: Name of the software; parsed from `/src/main/resources/info.properties`.
name - Variable in class model.Feature: An additional (human-readable) name for this feature.
NONE - Enum constant in enum class cli.CLISequence.Split: Do not split output files.
NUCLEOTIDE - Enum constant in enum class cli.CLISequence.Content: Nucleotide/genomic sequences.
NucleotideSequenceGenerator - Class in op: The NucleotideSequenceGenerator class is responsible for generating nucleotide sequences based on genomic data contained in a Storage instance.
NucleotideSequenceGenerator(Storage, Contig, boolean, boolean, Set<String>) - Constructor for class op.NucleotideSequenceGenerator: Constructs a new instance of the NucleotideSequenceGenerator class.
NucleotideSequenceGenerator(Storage, Contig, int, int, boolean, boolean, Set<String>) - Constructor for class op.NucleotideSequenceGenerator: Constructs a new instance of the NucleotideSequenceGenerator class with a specified interval.
NucleotideSequenceGenerator(Storage, Contig, Feature, boolean, boolean, Set<String>) - Constructor for class op.NucleotideSequenceGenerator: Constructs a new instance of the NucleotideSequenceGenerator class with a specified feature.
NUMBER_OF_ALLELES - Static variable in class util.Constants.AttributesKeys: Key representing the number of non-reference alleles associated with a feature.
NUMBER_OF_INDELS - Static variable in class util.Constants.AttributesKeys: Key representing the number of insertions and deletions (InDels) in a Sample.
NUMBER_OF_PROTEOFORMS - Static variable in class util.Constants.AttributesKeys: Key representing the number of non-reference proteoforms associated with a feature.
NUMBER_OF_SNVS - Static variable in class util.Constants.AttributesKeys: Key representing the number of substitutions or single nucleotide variants (SNVs) in a Sample.

O

ofAllele(String) - Method in class model.Variant: Checks if the variant is associated with a specific allele.
ofAlleles(Collection<String>) - Method in class model.Variant: Checks if the variant is associated with any of the specified alleles.
ofFeature(String) - Method in class model.Variant: Checks if the variant is associated with a specific feature.
ofFeatures(Collection<String>) - Method in class model.Variant: Checks if the variant is associated with any of the specified features.
ofSample(String) - Method in class model.Variant: Checks if the variant is associated with a specific sample.
ofSamples(Collection<String>) - Method in class model.Variant: Checks if the variant is associated with any of the specified samples.
op - package op: Implements atomic operations building the core functionality of the application.
options() - Static method in interface cli.CLI: Returns the command line options for this CLI component.
options() - Static method in class cli.CLIBuild: Defines the command-line options for the build task.
options() - Static method in class cli.CLIExpand: Defines the command-line options for the expand task.
options() - Static method in class cli.CLIProfile: Defines the command-line options for the view task.
options() - Static method in class cli.CLISequence: Defines the command-line options for the sequence task.
options() - Static method in class cli.CLIView: Defines the command-line options for the view task.
OS - Class in util: Utility class for operating system-related functionalities.
output - Variable in class cli.CLIBuild: The output path where the MUSIAL storage will be saved.
output - Variable in class cli.CLIExpand: The path to the output storage file.
output - Variable in class cli.CLIProfile: The path to the output destination.
output - Variable in class cli.CLIView: The path to the output destination.
OUTPUT_EXTENSION - Static variable in class main.Musial: File extension used for generated MUSIAL storage files.
outputGenerator - Variable in class cli.CLISequence: Generator for output paths per specified locus.
overwrite - Variable in class cli.CLIExpand: Indicates whether to overwrite the input file.

P

padGaps(String, int) - Static method in class util.Bio: Pads a string with gap characters to reach a specified length.
parameters - Variable in class model.Storage: Static parameters used by this storage.
Parameters(int, double, boolean, boolean, boolean, Map<String, Set<Integer>>) - Constructor for record class model.Storage.Parameters: Creates an instance of a Parameters record class.
PASS - Enum constant in enum class model.VariantCall.Flag: Indicates that the variant call has passed all filters.
PIPE - Static variable in class util.Constants: Pipe symbol string constant.
populateFromFeatures() - Method in class op.StorageTable: Populates the StorageTable.table with data of Features from the storage.
populateFromSamples() - Method in class op.StorageTable: Populates the StorageTable.table with data of Features from the storage.
populateFromVariants() - Method in class op.StorageTable: Populates the StorageTable.table with data of Variants from the storage.
populateWithAlleleProfile(boolean) - Method in class op.StorageTable: Populates the StorageTable.table with allele profile data from the storage.
populateWithProteoformProfile(boolean) - Method in class op.StorageTable: Populates the StorageTable.table with proteoform profile data from the storage.
populateWithVariantsProfile(boolean) - Method in class op.StorageTable: Populates the StorageTable.table with variant profile data from the storage.
position - Variable in class model.Variant: The 1-based position of this variant on a contig.
position() - Method in record class model.Variant.Stub: Returns the value of the position record component.
print(boolean) - Method in class op.StorageTable: Prints the contents of the StorageTable.table to the standard output.
printSoftwareInfo() - Static method in class util.Logging: Prints the software information to the console.
processFiles() - Method in class op.VCFProcessor: Analyzes the provided VCF files and processes their variant data.
PROFILE - Enum constant in enum class main.MusialTask: Task to profile samples by variants, alleles, or proteoforms.
Proteoform - Class in model: Represents a proteoform, which is a specific sequence type associated with a set of alleles.
Proteoform(List<Variant.Stub>) - Constructor for class model.Proteoform: Constructs a Proteoform instance with the specified variants.
PROTEOFORMS - Enum constant in enum class cli.CLIProfile.Content: Per sample proteoforms.

Q

query - Variable in class cli.CLIProfile: The set of query filters provided by the user.
query - Variable in class cli.CLIView: The set of query filters provided by the user.

R

randomAlphanumeric(int) - Static method in class util.IO: Generates a random alphanumeric string of the specified length.
read(ByteBuffer) - Method in class model.VariantCall.VariantCallSerializer: Deserializes a VariantCall object from a ByteBuffer.
readTabularFileAsNestedMap(File) - Static method in class util.IO: Reads a tabular file and converts its content into a nested map structure.
reduced - Variable in class cli.CLIProfile: Indicates whether to represent entries in a reduced format.
reference - Variable in class cli.CLIBuild: The reference sequence file used for variant annotation and typing.
reference - Variable in class model.Variant: The reference base content of this variant.
reference() - Method in record class model.VariantCall.CallAlternative: Returns the value of the reference record component.
REFERENCE - Static variable in class util.Constants: Term used for reference alleles in the context of Alleles.
REFERENCE_CALL - Enum constant in enum class model.VariantCall.Flag: Indicates that the variant call corresponds to the reference allele.
ReferenceContext(char, int) - Constructor for record class util.Bio.ReferenceContext: Creates an instance of a ReferenceContext record class.
removeAttribute(String) - Method in class model.Attributes: Removes an attribute with the specified key from this entity.
removeFeature(String) - Method in class model.Storage: Removes a feature from the storage by its unique identifier.
replaceFeature(Feature, Feature) - Method in class model.Storage: Replaces an existing feature in the storage with a new feature.
run() - Method in class task.ExecutorBuild: Executes the main logic of the build task.
run() - Method in class task.ExecutorExpand: Executes the main logic of the expand task.
run() - Method in class task.ExecutorProfile: Executes the main logic of the ExecutorProfile class.
run() - Method in class task.ExecutorSequence: Executes the sequence generation task based on the specified content type.
run() - Method in class task.ExecutorView: Executes the main logic of the view task.
runCommand(String[], String, String, String) - Static method in class util.OS: Executes a command-line command using a ProcessBuilder.
runSnpEff(Path) - Method in class op.VariantAnnotator: Runs variant annotation using SnpEff on the Storage.

S

Sample - Class in model: Represents a single biological sample.
Sample(String, int) - Constructor for class model.Sample: Constructs a new Sample instance with the specified id and initial capacity for the alleles map.
SAMPLE - Enum constant in enum class cli.CLISequence.Split: Split output files by sample (or sequence type) identifier.
samples - Variable in class cli.CLISequence: The set of sample identifiers provided by the user.
SAMPLES - Enum constant in enum class cli.CLIView.Content: The samples of the storage.
SEMICOLON - Static variable in class util.Constants: Semicolon string constant.
SEQUENCE - Enum constant in enum class main.MusialTask: Task to export sequence data in FASTA format from a MUSIAL storage file.
SEQUENCE_LENGTH_DEVIATION - Static variable in class util.Constants.AttributesKeys: Key representing the net shift in sequence length of a SequenceType.
SEQUENCE_ONTOLOGY_HIERARCHY - Static variable in class model.Storage: A static map defining the hierarchy levels of Sequence Ontology (SO) terms used in the model.
sequenceCache - Variable in class model.Contig: Cache to store the (sub-)sequence of this contig given a start and end position.
SequenceGenerator - Interface in op: Interface for generating sequences based on a sample identifier.
SequenceType - Class in model: Represents a sequence type with associated variants and attributes.
serialize(VariantCall) - Method in class model.VariantCall.VariantCallSerializer: Serializes a VariantCall object into a ByteBuffer.
setAttribute(String, String) - Method in class model.Attributes: Adds an attribute to this entity.
setAttributeIfAbsent(String, String) - Method in class model.Attributes: Adds an attribute to this entity only if it does not already exist.
setAttributes(Map<String, String>) - Method in class model.Attributes: Adds multiple attributes to this entity.
setAttributesIfAbsent(Map<String, String>) - Method in class model.Attributes: Adds multiple attributes to this entity only if they do not already exist.
setFilters(Set<String>) - Method in class op.StorageTable: Sets filters for building the table based on the provided query strings.
setProteoformRelation(String) - Method in class model.Allele: Sets the proteoform identifier for this allele.
setReference(IndexedFastaSequenceFile) - Method in class model.Storage: Sets the reference sequence for the storage and populates contigs based on the reference.
SIGN - Static variable in class util.Constants: Number sign string constant.
skipAnnotation - Variable in class cli.CLIBuild: If annotation of variants is skipped during the build process.
skipAnnotation() - Method in record class model.Storage.Parameters: Returns the value of the skipAnnotation record component.
skipTyping - Variable in class cli.CLIBuild: If typing of samples is skipped during the build process.
skipTyping() - Method in record class model.Storage.Parameters: Returns the value of the skipTyping record component.
SNP_EFF_KEYS - Static variable in class util.Constants: SnpEff annotation field names.
SNP_EFF_PREFIX - Static variable in class util.Constants: Prefix for SnpEff attribute keys.
SNV - Enum constant in enum class model.Variant.Type: Single Nucleotide Variant.
SO_EFFECTS - Static variable in class util.Constants.AttributesKeys: Key representing the Sequence-Ontology effects associated with a SequenceType.
split - Variable in class cli.CLISequence: The mode to split output files by.
start - Variable in class model.Feature: 1-based starting position of the feature.
start() - Method in record class model.Feature.SubFeature: Returns the value of the start record component.
start() - Method in record class op.VCFProcessor.UpstreamDeletion: Returns the value of the start record component.
startTime - Static variable in class main.Musial: Start time of the program.
Storage - Class in model: Central component of the MUSIAL model, designed to manage genomic data, including contigs, features, and samples.
Storage(Storage.Parameters) - Constructor for class model.Storage: Constructs a new Storage instance with the specified parameters.
Storage.Parameters - Record Class in model: The parameters used for configuring the storage of variant data.
StorageFactory - Class in op: Factory class for creating and loading Storage objects.
StorageIO - Class in op: The StorageIO class provides utility methods for serializing and deserializing genomic data.
StorageTable - Class in op: The StorageTable class provides functionality to create and manage tabular representations of genomic data stored in a Storage instance using the tablesaw library.
StorageTable(Storage) - Constructor for class op.StorageTable: Constructs an instance of the StorageTable class with the specified storage.
StorageUpdater - Class in op: Encapsulates complex update logic for genomic data storage from the Storage class itself.
StorageUpdater(Storage) - Constructor for class op.StorageUpdater: Constructs a new StorageUpdater instance.
strand - Variable in class model.Feature: Strand of the feature.
stripGaps(String) - Static method in class util.Bio: Removes all gap characters from the input string.
Stub(int, String) - Constructor for record class model.Variant.Stub: Creates an instance of a Stub record class.
SubFeature(String, int, int) - Constructor for record class model.Feature.SubFeature: Creates an instance of a SubFeature record class.
SYNONYMOUS - Static variable in class util.Constants: Term used for synonymous proteoforms in the context of Proteoforms.

T

TAB - Static variable in class util.Constants: Tabulator string constant.
task - package task: Implements tasks that represent high-level workflows of the application, each encapsulating a specific sequence of operations.
task - Static variable in class main.Musial: Specifies the task to execute.
tempDir - Static variable in class main.Musial: Temporary directory for intermediate files.
TERMINAL_AA - Static variable in class util.Constants: Translated stop codon in an amino acid sequence.
toFASTA(Storage) - Static method in class op.StorageIO: Generates the content of a FASTA file from the given Storage object.
toGFF3(Storage) - Static method in class op.StorageIO: Generates the content of a GFF (General Feature Format) file from the given Storage object.
toJSON(Storage, Path) - Static method in class op.StorageIO: Serializes the given Storage object to a JSON file at the specified path.
toString() - Method in class model.Allele: Converts the allele to its string representation.
toString() - Method in class model.Contig: Returns the string representation of this contig.
toString() - Method in record class model.Feature.SubFeature: Returns a string representation of this record class.
toString() - Method in class model.Feature: Generates a string representation of this feature.
toString() - Method in class model.Proteoform: Converts the proteoform to its string representation.
toString() - Method in class model.Sample: Converts the sample to its string representation.
toString() - Method in record class model.Storage.Parameters: Returns a string representation of this record class.
toString() - Method in record class model.Variant.Stub: Converts the variant stub to its string representation.
toString() - Method in class model.Variant: Converts the variant to its string representation.
toString() - Method in record class model.VariantCall.CallAlternative: Converts the alternative allele to its string representation.
toString() - Method in record class model.VariantCall: Converts the variant call to its string representation.
toString() - Method in record class op.VCFProcessor.UpstreamDeletion: Returns a string representation of this record class.
toString() - Method in record class util.Bio.ReferenceContext: Returns a string representation of this record class.
toVCF(Storage, boolean, boolean) - Static method in class op.StorageIO: Generates the content of a VCF (Variant Call Format) file from the given Storage object.
translateSequence(String, boolean) - Static method in class util.Bio: Translates a DNA sequence into an amino-acid sequence.
type - Variable in class model.Feature: The type of this genomic feature.
type - Variable in class model.Variant: The type of this variant (e.g., SNV, insertion, deletion).
type() - Method in record class model.Feature.SubFeature: Returns the value of the type record component.
typeAdapter() - Static method in class model.Storage: Creates a custom TypeAdapter for the Storage class.

U

UNDEFINED - Enum constant in enum class main.MusialTask: Task is undefined.
UNDER_SCORE - Static variable in class util.Constants: Underscore string constant.
UNDERSCORE - Static variable in class util.Constants: Underscore string constant.
updateSampleAttributes(Map<String, Map<String, String>>) - Method in class op.StorageUpdater: Updates the attributes of samples in the storage.
updateSequenceTypes() - Method in class op.StorageUpdater: Updates the sequence types for all features and samples in the storage.
updateStatistics() - Method in class op.StorageUpdater: Updates statistical attributes for samples, contigs, and features in the storage.
updateVariants() - Method in class op.VCFProcessor: Updates the variants in the storage by processing variant calls from the cache.
UPSTREAM_DELETION - Enum constant in enum class model.VariantCall.Flag: Indicates that the variant call is missing due to an upstream deletion.
UpstreamDeletion(String, int, int, boolean) - Constructor for record class op.VCFProcessor.UpstreamDeletion: Creates an instance of a UpstreamDeletion record class.
util - package util: Implements utility classes and methods for the application.

V

validateContig(Storage, Contig, boolean) - Method in class op.AminoacidSequenceGenerator: Validates the provided contig to ensure it is suitable for amino acid sequence generation.
validateFeature(Storage, Feature) - Method in class op.AminoacidSequenceGenerator: Validates the provided feature to ensure it is suitable for amino acid sequence generation.
validateFeatures() - Method in class op.FeatureLoader: Validates the features stored in the storage to ensure compliance with Sequence Ontology (SO) hierarchy rules.
valueOf(String) - Static method in enum class cli.CLIProfile.Content: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class cli.CLISequence.Content: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class cli.CLISequence.Split: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class cli.CLIView.Content: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class main.MusialTask: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class model.Variant.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class model.VariantCall.Flag: Returns the enum constant of this class with the specified name.
values() - Static method in enum class cli.CLIProfile.Content: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class cli.CLISequence.Content: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class cli.CLISequence.Split: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class cli.CLIView.Content: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class main.MusialTask: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class model.Variant.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class model.VariantCall.Flag: Returns an array containing the constants of this enum class, in the order they are declared.
variable - Variable in class cli.CLISequence: Indicates whether only variable sites should be considered.
Variant - Class in model: Represents a nucleotide variant.
Variant(int, String, String) - Constructor for class model.Variant: Constructs a new Variant instance, based on the provided position, reference, and alternative content.
VARIANT_FREQUENCY - Static variable in class util.Constants.AttributesKeys: Key representing the frequency of a Variant across all stored samples.
Variant.Stub - Record Class in model: Represents a simplified variant stub with position and alternative allele information.
Variant.Type - Enum Class in model: Enum representing the type of variant.
VariantAnnotator - Class in op: The VariantAnnotator class provides functionality to annotate variants.
VariantAnnotator(Storage) - Constructor for class op.VariantAnnotator: Constructs a new instance of the VariantAnnotator class.
VariantCall - Record Class in model: Represents a variant call in a biological sample.
VariantCall(VariantCall.Flag, short, float, List<VariantCall.CallAlternative>) - Constructor for record class model.VariantCall: Creates an instance of a VariantCall record class.
VariantCall.CallAlternative - Record Class in model: Represents one alternative in the context of a variant call.
VariantCall.Flag - Enum Class in model: Enumeration of flags representing the status of a variant call.
VariantCall.VariantCallSerializer - Class in model: Serializer for the VariantCall class.
VariantCallSerializer() - Constructor for class model.VariantCall.VariantCallSerializer: Constructs a new VariantCall.VariantCallSerializer instance.
VARIANTS - Enum constant in enum class cli.CLIProfile.Content: Per sample variants.
VARIANTS - Enum constant in enum class cli.CLIView.Content: The variants of the storage.
vcfFiles - Variable in class cli.CLIBuild: The list of VCF files to be processed.
vcfFiles - Variable in class cli.CLIExpand: The list of VCF file paths to expand the storage with.
vcfMeta - Variable in class cli.CLIBuild: A map containing the VCF metadata, with the sample ID as the key and another map of metadata attributes and their values as the
vcfMeta - Variable in class cli.CLIExpand: A map containing the VCF metadata, with the sample ID as the key and another map of metadata attributes and their values as the
VCFProcessor - Class in op: The VCFProcessor class is responsible for processing Variant Call Format (VCF) files.
VCFProcessor(List<Path>, Storage, boolean) - Constructor for class op.VCFProcessor: Constructs a new VCFProcessor instance for processing VCF files.
VCFProcessor.UpstreamDeletion - Record Class in op: Represents an upstream deletion affecting a sample.
version - Static variable in class main.Musial: Version of the software; parsed from `/src/main/resources/info.properties`.
VIEW - Enum constant in enum class main.MusialTask: Task to generate tables of various content from a MUSIAL storage file.

W

write() - Method in class op.StorageTable: Writes the current StorageTable.table to a TSV file in the current user directory at System.getProperty("user.dir").
write(String, char) - Method in class op.StorageTable: Writes the current StorageTable.table to a tabular file with the specified separator.
writeFile(Path, String) - Static method in class util.IO: Writes the specified content to a file at the given path.

_

_id - Variable in class model.Contig: Unique identifier of this contig.
_id - Variable in class model.Feature: Unique identifier of this feature.
_id - Variable in class model.Sample: Unique identifier of this sample.
_id - Variable in class model.SequenceType: Unique identifier of this sequence type.

A B C D E F G H I L M N O P Q R S T U V W _
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