Package org.monarchinitiative.lirical.cli.cmd

package org.monarchinitiative.lirical.cli.cmd

Commands to run LIRICAL in different configurations.

Related Packages

Package	Description
org.monarchinitiative.lirical.cli
org.monarchinitiative.lirical.cli.cmd.experimental	Package with experimental LIRICAL commands.
org.monarchinitiative.lirical.cli.cmd.util
org.monarchinitiative.lirical.cli.yaml	Read user input formatted into YAML file.

Class	Description
BenchmarkCommand	Benchmark command runs LIRICAL on one or more phenopackets and writes prioritization results into a CSV table.
DownloadCommand	Download a number of files needed for the analysis.
OutputCommand
OutputCommand.Output
PhenopacketCommand	Run LIRICAL from a Phenopacket -- with or without accompanying VCF file.
PhenopacketUtil
PrioritizeCommand
ValidationPolicy	What to do in case of errors or imperfections in the input data.
YamlCommand	This class coordinates the main analysis of a VCF file plus list of observed HPO terms.