LIRICAL 2.0.2 API
Packages
Package
Description
Classes related to calculating the distribution of pathogenicity scores of ClinVar or all GNOMAD variants.
Commands to run LIRICAL in different configurations.
Package with experimental LIRICAL commands.
Read user input formatted into YAML file.
Core functionality of the LIRICAL algorithm.
A high-level representation of LIRICAL analysis.
Default LIRICAL analysis implementation.
Model of pretest probability of diseases.
Top-level exceptions.
APIs for reading and annotation of genomic variants.
Package with logic for calculation of likelihood ratios for phenotypic or genotypic test results.
Classes in this package were slightly adapted from the Apache Math version 3 library and remain under the
Apache License, Version 2.0.
Package with data models.
Base data model for writing out the results of LIRICAL analysis.
Sanitize the user-provided
SanitationInputs.Package with services used across LIRICAL.
Package with utility methods such as binary search with custom comparator for extracting the sorting key.
Parsers for LIRICAL.
Read user input formatted as a v1 or v2 phenopacket.
Classes for writing out LIRICAL analysis results into HTML, TSV, and JSON files.
Classes to create an SVG graphic representing the result of likelihood raio analysis of one HPO Case.