Package picard.arrays
Class CollectArraysVariantCallingMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.arrays.CollectArraysVariantCallingMetrics
Collects summary and per-sample metrics about variant calls in a VCF file.
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
static class
static class
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Field Summary
FieldsFields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, 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
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Method Summary
Modifier and TypeMethodDescriptionprotected String[]
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.static boolean
getSexConcordance
(String reportedSexString, String fingerprintSexString, String autocallSexString) Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, 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
@Argument(shortName="O", doc="Path (except for the file extension) of output metrics files to write.") public File OUTPUT -
CALL_RATE_PF_THRESHOLD
@Argument(doc="The Call Rate Threshold for an autocall pass (if the observed call rate is > this value, the sample is considered to be passing)", optional=true) public static Double CALL_RATE_PF_THRESHOLD -
DBSNP
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SEQUENCE_DICTIONARY
@Argument(shortName="SD", optional=true, doc="If present, speeds loading of dbSNP file, will look for dictionary in vcf if not present here.") public File SEQUENCE_DICTIONARY -
NUM_PROCESSORS
@Argument(doc="Split this task over multiple threads. If NUM_PROCESSORS = 0, number of cores is automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0 then the number of cores used will be the number available on the machine less NUM_PROCESSORS.") public int NUM_PROCESSORS
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Constructor Details
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CollectArraysVariantCallingMetrics
public CollectArraysVariantCallingMetrics()
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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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customCommandLineValidation
Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
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getSexConcordance
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