Package picard.reference
Class NormalizeFasta
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.reference.NormalizeFasta
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@DocumentedFeature public class NormalizeFasta extends CommandLineProgram
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
Fields Modifier and Type Field Description File
INPUT
int
LINE_LENGTH
File
OUTPUT
boolean
TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description NormalizeFasta()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.static void
main(String[] args)
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Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(shortName="I", doc="The input FASTA file to normalize.") public File INPUT
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OUTPUT
@Argument(shortName="O", doc="The output FASTA file to write.") public File OUTPUT
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LINE_LENGTH
@Argument(doc="The line length to be used for the output FASTA file.") public int LINE_LENGTH
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TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE
@Argument(doc="Truncate sequence names at first whitespace.") public boolean TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE
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Method Detail
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main
public static void main(String[] args)
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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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