Package picard.reference
Class NormalizeFasta
java.lang.Object
picard.cmdline.CommandLineProgram
picard.reference.NormalizeFasta
Little program to "normalize" a fasta file to ensure that all line of sequence are the
same length, and are a reasonable length!
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Field Summary
FieldsModifier and TypeFieldDescriptionint
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.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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LINE_LENGTH
@Argument(doc="The line length to be used for the output FASTA file.") public int LINE_LENGTH -
TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE
@Argument(doc="Truncate sequence names at first whitespace.") public boolean TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE
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Constructor Details
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NormalizeFasta
public NormalizeFasta()
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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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