Package picard.vcf
Class FixVcfHeader
java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.FixVcfHeader
Tool for replacing or fixing up a VCF header.
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Field Summary
FieldsModifier and TypeFieldDescriptionint
boolean
Fields 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
Constructors -
Method Summary
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
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CHECK_FIRST_N_RECORDS
@Argument(shortName="N", doc="Check only the first N records when searching for missing INFO and FORMAT fields.", optional=true) public int CHECK_FIRST_N_RECORDS -
HEADER
@Argument(shortName="H", doc="The replacement VCF header.", optional=true) public PicardHtsPath HEADER -
ENFORCE_SAME_SAMPLES
@Argument(doc="Enforce that the samples are the same (and in the same order) when replacing the VCF header.", optional=true) public boolean ENFORCE_SAME_SAMPLES
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Constructor Details
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FixVcfHeader
public FixVcfHeader()
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Method Details
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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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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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