Package org.monarchinitiative.lirical.cli.cmd

Class OutputCommand

java.lang.Object

org.monarchinitiative.lirical.cli.cmd.OutputCommand

All Implemented Interfaces:

Callable<Integer>

Direct Known Subclasses:

PhenopacketCommand, PhenopacketsCommand, PrioritizeCommand, YamlCommand

public abstract class OutputCommand
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	OutputCommand.Output

Field Summary

Fields

Modifier and Type	Field	Description
org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.DataSection	dataSection
OutputCommand.Output	output
org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.RunConfiguration	runConfiguration
protected static final String	UNKNOWN_VERSION_PLACEHOLDER
boolean[]	verbosity

Constructor Summary

Constructors

Constructor	Description
OutputCommand()

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 OutputOptions	createOutputOptions(String prefix)
protected abstract Integer	execute()
protected String	figureOutExomiserPath()
protected abstract 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

output

public OutputCommand.Output output

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

OutputCommand

public OutputCommand()

Method Details

checkInput

protected List<String> checkInput()

createOutputOptions

protected OutputOptions createOutputOptions(String prefix)

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

getGenomeBuild

protected abstract String getGenomeBuild()

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>

execute

protected abstract Integer execute()