picard.reference

Class NormalizeFasta

java.lang.Object

picard.cmdline.CommandLineProgram

picard.reference.NormalizeFasta

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!

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
int	LINE_LENGTH
java.io.File	OUTPUT
boolean	TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
NormalizeFasta()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args)

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT

@Option(shortName="I",
        doc="The input FASTA file to normalize.")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="The output FASTA file to write.")
public java.io.File OUTPUT

LINE_LENGTH

@Option(doc="The line length to be used for the output FASTA file.")
public int LINE_LENGTH

TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE

@Option(doc="Truncate sequence names at first whitespace.")
public boolean TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE

Constructor Detail

NormalizeFasta

public NormalizeFasta()

Method Detail

main

public static void main(java.lang.String[] args)

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 class CommandLineProgram

Returns:

program exit status.