Package org.monarchinitiative.lirical.cli.cmd

Class BenchmarkCommand

java.lang.Object

org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand

All Implemented Interfaces:

Callable<Integer>

public class BenchmarkCommand
extends Object

Benchmark command runs LIRICAL on one or more phenopackets and writes prioritization results into a CSV table. Optionally, a VCF file with background variants can be provided to run variant-aware prioritization. In presence of variants, the benchmark spikes the variants from phenopacket into the background variants and runs prioritization on phenotype terms and variants.

Field Summary

Fields

Modifier and Type	Field	Description
org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.DataSection	dataSection
protected String	genomeBuild
protected Path	outputPath
protected List<Path>	phenopacketPaths
protected boolean	phenotypeOnly	Deprecated, for removal: This API element is subject to removal in a future version.
org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.RunConfiguration	runConfiguration
protected static final String	UNKNOWN_VERSION_PLACEHOLDER
protected Path	vcfPath
boolean[]	verbosity

Constructor Summary

Constructors

Constructor	Description
BenchmarkCommand()

Method Summary

Modifier and Type	Method	Description
protected Lirical	bootstrapLirical(GenomeBuild genomeBuild)	Build Lirical for a GenomeBuild based on LiricalConfigurationCommand.DataSection and LiricalConfigurationCommand.RunConfiguration sections.
Integer	call()
protected List<String>	checkInput()
Integer	execute()
protected String	figureOutExomiserPath()
protected String	getGenomeBuild()
protected AnalysisOptions	prepareAnalysisOptions(Lirical lirical, GenomeBuild genomeBuild, TranscriptDatabase transcriptDb)	Prepare the options for parametrizing the analysis.
protected static org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.SampleIdAndGenesAndGenotypes	readVariantsFromVcfFile(String sampleId, Path vcfPath, GenomeBuild genomeBuild, TranscriptDatabase transcriptDatabase, VariantParserFactory parserFactory)
protected static void	reportElapsedTime(long startTime, long stopTime)
protected InputSanitizer	selectSanitizer(InputSanitizerFactory factory)
protected static String	summarizeSanitationResult(SanitationResult sanitationResult)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

phenopacketPaths

protected List<Path> phenopacketPaths

vcfPath

protected Path vcfPath

outputPath

protected Path outputPath

phenotypeOnly

@Deprecated(since="2.1.1",
            forRemoval=true)
protected boolean phenotypeOnly

Deprecated, for removal: This API element is subject to removal in a future version.

genomeBuild

protected String genomeBuild

UNKNOWN_VERSION_PLACEHOLDER

protected static final String UNKNOWN_VERSION_PLACEHOLDER

See Also:

• Constant Field Values

dataSection

public org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.DataSection dataSection

runConfiguration

public org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.RunConfiguration runConfiguration

verbosity

public boolean[] verbosity

Constructor Details

BenchmarkCommand

public BenchmarkCommand()

Method Details

execute

public Integer execute()

checkInput

protected List<String> checkInput()

getGenomeBuild

protected String getGenomeBuild()

bootstrapLirical

protected Lirical bootstrapLirical(GenomeBuild genomeBuild)
                            throws LiricalDataException

Build Lirical for a GenomeBuild based on LiricalConfigurationCommand.DataSection and LiricalConfigurationCommand.RunConfiguration sections.

Parameters:

genomeBuild - the target build or null if LIRICAL should be configured in phenotype-only mode.

Throws:

LiricalDataException

prepareAnalysisOptions

protected AnalysisOptions prepareAnalysisOptions(Lirical lirical,
 GenomeBuild genomeBuild,
 TranscriptDatabase transcriptDb)

Prepare the options for parametrizing the analysis.

Parameters:

genomeBuild - a build or null if running in phenotype-only mode.

readVariantsFromVcfFile

protected static org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.SampleIdAndGenesAndGenotypes readVariantsFromVcfFile(String sampleId,
 Path vcfPath,
 GenomeBuild genomeBuild,
 TranscriptDatabase transcriptDatabase,
 VariantParserFactory parserFactory)
                                                                                                                                 throws LiricalParseException

Throws:

LiricalParseException

summarizeSanitationResult

protected static String summarizeSanitationResult(SanitationResult sanitationResult)

figureOutExomiserPath

protected String figureOutExomiserPath()

selectSanitizer

protected InputSanitizer selectSanitizer(InputSanitizerFactory factory)

reportElapsedTime

protected static void reportElapsedTime(long startTime,
 long stopTime)

call

public Integer call()

Specified by:

call in interface Callable<Integer>