Package picard.fingerprint
Class CalculateFingerprintMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.fingerprint.CalculateFingerprintMetrics
Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have.
For example, if too many sites are heterozygous, that would get flagged.
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Field Summary
FieldsModifier and TypeFieldDescriptionfinal double
final int
boolean
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
doWork()
Do the work after command line has been parsed.getFingerprintMetrics
(Fingerprint fingerprint) Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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INPUT
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OUTPUT
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HAPLOTYPE_MAP
@Argument(shortName="H", doc="The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.") public File HAPLOTYPE_MAP -
CALCULATE_BY
@Argument(doc="Specificies which data-type should be used as the basic unit. Fingerprints from readgroups can be \"rolled-up\" to the LIBRARY, SAMPLE, or FILE level before being used. Fingerprints from VCF can be be examined by SAMPLE or FILE.") public CrosscheckMetric.DataType CALCULATE_BY -
GENOTYPE_LOD_THRESHOLD
@Argument(doc="LOD score threshold for considering a genotype to be definitive.") public final double GENOTYPE_LOD_THRESHOLD- See Also:
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NUMBER_OF_SAMPLING
@Argument(doc="Number of randomization trials for calculating the DISCRIMINATORY_POWER metric.") public final int NUMBER_OF_SAMPLING- See Also:
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TEST_INPUT_READABILITY
@Hidden @Argument(doc="When true code will check for readability on input files (this can be slow on cloud access)") public boolean TEST_INPUT_READABILITY
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Constructor Details
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CalculateFingerprintMetrics
public CalculateFingerprintMetrics()
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Method Details
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doWork
protected int doWork()Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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getFingerprintMetrics
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