All Classes and Interfaces
Class
Description
Convenience class to represent the age of a subject.
Specialised
DataType for (de)serialising AlleleProto.AlleleProperties objects into and out of
the MVStore.Protobuf type
AlleleKeyProtobuf type
AlleleKeyProtobuf type
AllelePropertiesProtobuf type
AllelePropertiesProtobuf type
ClinVarProtobuf type
ClinVarProtobuf enum
ClinVar.ClinSigRepresentation of subject data required by LIRICAL analysis.
A container for analysis-specific settings, i.e.
A builder for
AnalysisOptions.A container for the likelihood ratio test results.
The implementors can store results of LIRICAL analysis in some
OutputFormat.Factory class for getting
AnalysisResultsWriters.This command is used to generate the background frequency files.
This class coordinates the input of the background frequency file.
Benchmark command runs LIRICAL on one or more phenopackets and writes prioritization results into a CSV table.
Static utility class with the binary search implementation for arrays of items with custom key extractor function.
CADD info - see here.
A subset of ClinVar allele data relevant for LIRICAL analysis.
Clinvar clinical significance categories.
Immutable data class representing data from the ClinVar resource, with
explanation of the data from https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
A
BackgroundVariantFrequencyServiceFactory implementation that uses user-provided frequency files.This class stores all the information we need for a detailed differential diagnosis -- the major
candidates.
Download a number of files needed for the analysis.
A summary of variant input and functional annotation.
Frequency data for the variant from the Thousand Genomes, the Exome Server
Project and Broad ExAC datasets.
Enum describing where the frequency data has originated.
FunctionalVariantAnnotatorService knows about
FunctionalVariantAnnotators for all genome build
and transcript database combinations that have been configured for a given
Lirical instance.Gene2Genotype represents variants that have been annotated to a single gene.
Container for
Gene2Genotypes present in the analysis.This class calculates the relative proportions of variants assessed as having a certain degree of pathogenicity
by Exomiser.
A description of variant coordinates, sample genotypes, and filtering status for LIRICAL analysis.
This class is responsible for calculating the likelihood ratio for genotypes, as described
in the Material and Methods | Likelihood Ratio for Genotypes section
of the LIRICAL manuscript.
The enum for representing the type of the genotype likelihood ratio analysis performed for a gene.
Results of genotype likelihood ratio evaluation for a single gene.
This class coordinates getting the data from the analysis into the FreeMark org.monarchinitiative.lirical.output templates.
This class arranges data for genes that do not have a probable differential diagnosis.
For some calculations of the phenotype likelihood ratio, we need to traverse the graph induced by the HPO terms to
which a disease is annotated.
Sanitize the user input before running the analysis.
Get the input sanitizer with required level
An exception thrown by
LiricalAnalysisRunner if the analysis
cannot be run.The analysis runner runs LIRICAL analysis on provided analysis subject (
AnalysisData).An exception thrown when data error (missing resource, invalid resource file, etc.) is detected.
Global options to parameterize LIRICAL execution.
An exception thrown when user-provided input is invalid.
This is the superclass for
TsvTemplate and HtmlTemplate, and provides common methods for
setting up the data prior to output as either tab-separated values (TSV) or HTML.This class creates an SVG file representing the results of likelihood ratio analysis of an HPO case.
This class encapsulates the likelihood ratio threshold, which is an optional user argument (-t).
There are five possible ways that a query term can match a disease term.
This class encapsulates the minimum number of diagnoses to show, which is an optional user argument (-m).
A deleteriousness prediction score for missense variants based on regional missense constraint.
Utility class for helping read and write Alleles to the
MVStoreA
VariantMetadataService implementation used when the variant data is not available.LIRICAL supports writing results in these formats.
Container for Pathogenicity data about a variant.
Enum representing the pathogenicity prediction method/database used to
calculate a given score.
Run LIRICAL from a Phenopacket -- with or without accompanying VCF file.
Phenopacket attributes that are relevant for LIRICAL.
Decode phenopacket data from an input stream.
Get
PhenopacketImporters to ingest v1 or v2 phenopackets.Run LIRICAL in phenotype-only mode on a collection of phenopackets.
This class is designed to calculate the background and foreground frequencies of any HPO term in any disease
(This is calculated by
PhenotypeLikelihoodRatio.initializeFrequencyMap() and stored in PhenotypeLikelihoodRatio.hpoTerm2OverallFrequency).This class and the other classes in this package were adapted and mainly copied from the
Apache Math package.
PolyPhen (polymorphism phenotyping) score.
A collection of
PretestDiseaseProbability instances.Implementors provide pretest probability for observing a disease.
Class for pretty progress reporting using logger.
REMM info.
Immutable value Class representing an NCBI dbSNP reference SNP rsID.
A container for associating sample id and the
AlleleCount.The sanitation requirements.
Result of the input sanitation.
Result of input sanitation.
Enum to represent the existing sanitizer types.
An issue that was found in the analysis input.
Represents the severity of an issue found during input data sanitation.
The score is the normalized probability that the amino acid change is
tolerated.
Make a set of sparklines for the top of the page.
This class encapsulates all of the information we need to produce one row of the sparkline table.
This class organizes information about the result of a test.
The interface represents variant functional annotation data required by LIRICAL.
This class coordinates the output of a TSV file that contains a suymmary of the analysis results.
What to do in case of errors or imperfections in the input data.
Set of constants for use as default pathogenicity scores for a given
VariantEffect.VariantMetadataServiceFactory knows about
VariantMetadataServices for all genome builds
that have been configured for a given Lirical instance.Class to represent pathogenicity data available for a genomic variant.
The variant data for displaying in SVG widget.
This class coordinates the main analysis of a VCF file plus list of observed HPO terms.
This class is used to input the YAML configuration file.
This class ingests a YAML file with parameters that will be used for the analysis.