Package org.monarchinitiative.lirical.cli.cmd

Class PhenopacketCommand

java.lang.Object

org.monarchinitiative.lirical.cli.cmd.OutputCommand

org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand

All Implemented Interfaces:

Callable<Integer>

public class PhenopacketCommand
extends OutputCommand

Run LIRICAL from a Phenopacket -- with or without accompanying VCF file.

Author:

Peter N Robinson

Nested Class Summary

Nested classes/interfaces inherited from class org.monarchinitiative.lirical.cli.cmd.OutputCommand

OutputCommand.Output

Field Summary

Fields

Modifier and Type	Field	Description
org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.DataSection	dataSection
String	genomeBuild
Path	phenopacketPath
org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.RunConfiguration	runConfiguration
protected static final String	UNKNOWN_VERSION_PLACEHOLDER
Path	vcfPath
boolean[]	verbosity

Fields inherited from class org.monarchinitiative.lirical.cli.cmd.OutputCommand

output

Constructor Summary

Constructors

Constructor	Description
PhenopacketCommand()

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()
protected static String	checkVcfAndAssembly(Path vcfPath, String genomeBuild)
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 SanitationInputs	procureSanitationInputs()
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 org.monarchinitiative.lirical.cli.cmd.OutputCommand

createOutputOptions

Methods inherited from class java.lang.Object

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

Field Details

genomeBuild

public String genomeBuild

phenopacketPath

public Path phenopacketPath

vcfPath

public Path vcfPath

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

PhenopacketCommand

public PhenopacketCommand()

Method Details

getGenomeBuild

protected String getGenomeBuild()

procureSanitationInputs

protected SanitationInputs procureSanitationInputs()
                                            throws LiricalParseException

Throws:

LiricalParseException

checkInput

protected List<String> checkInput()

Overrides:

checkInput in class OutputCommand

execute

public Integer execute()

checkVcfAndAssembly

protected static String checkVcfAndAssembly(Path vcfPath,
 String genomeBuild)

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>