Class PhenopacketCommand
java.lang.Object
org.monarchinitiative.lirical.cli.cmd.OutputCommand
org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
Run LIRICAL from a Phenopacket -- with or without accompanying VCF file.
- Author:
- Peter N Robinson
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Nested Class Summary
Nested classes/interfaces inherited from class org.monarchinitiative.lirical.cli.cmd.OutputCommand
OutputCommand.Output
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Field Summary
FieldsModifier and TypeFieldDescriptionorg.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.DataSection
org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.RunConfiguration
protected static final String
boolean[]
Fields inherited from class org.monarchinitiative.lirical.cli.cmd.OutputCommand
output
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected Lirical
bootstrapLirical
(GenomeBuild genomeBuild) BuildLirical
for aGenomeBuild
based onLiricalConfigurationCommand.DataSection
andLiricalConfigurationCommand.RunConfiguration
sections.call()
protected static String
checkVcfAndAssembly
(Path vcfPath, String genomeBuild) execute()
protected String
protected String
protected AnalysisOptions
prepareAnalysisOptions
(Lirical lirical, GenomeBuild genomeBuild, TranscriptDatabase transcriptDb) Prepare the options for parametrizing the analysis.protected SanitationInputs
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
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Field Details
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genomeBuild
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phenopacketPath
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vcfPath
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UNKNOWN_VERSION_PLACEHOLDER
- See Also:
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dataSection
public org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.DataSection dataSection -
runConfiguration
public org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.RunConfiguration runConfiguration -
verbosity
public boolean[] verbosity
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Constructor Details
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PhenopacketCommand
public PhenopacketCommand()
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Method Details
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getGenomeBuild
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procureSanitationInputs
- Throws:
LiricalParseException
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checkInput
- Overrides:
checkInput
in classOutputCommand
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execute
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checkVcfAndAssembly
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bootstrapLirical
BuildLirical
for aGenomeBuild
based onLiricalConfigurationCommand.DataSection
andLiricalConfigurationCommand.RunConfiguration
sections.- Parameters:
genomeBuild
- the target build ornull
if LIRICAL should be configured in phenotype-only mode.- Throws:
LiricalDataException
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prepareAnalysisOptions
protected AnalysisOptions prepareAnalysisOptions(Lirical lirical, GenomeBuild genomeBuild, TranscriptDatabase transcriptDb) Prepare the options for parametrizing the analysis.- Parameters:
genomeBuild
- a build ornull
if running in phenotype-only mode.
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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
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summarizeSanitationResult
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figureOutExomiserPath
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selectSanitizer
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reportElapsedTime
protected static void reportElapsedTime(long startTime, long stopTime) -
call
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