picard.reference

Class ExtractSequences

java.lang.Object

picard.cmdline.CommandLineProgram

picard.reference.ExtractSequences

@DocumentedFeature
public class ExtractSequences
extends CommandLineProgram

Simple command line program that allows sub-sequences represented by an interval list to be extracted from a reference sequence file.

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INTERVAL_LIST
int	LINE_LENGTH
java.io.File	OUTPUT

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, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
ExtractSequences()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
protected boolean	requiresReference()

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

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

Field Detail

INTERVAL_LIST

@Argument(doc="Interval list describing intervals to be extracted from the reference sequence.")
public java.io.File INTERVAL_LIST

OUTPUT

@Argument(shortName="O",
          doc="Output FASTA file.")
public java.io.File OUTPUT

LINE_LENGTH

@Argument(doc="Maximum line length for sequence data.")
public int LINE_LENGTH

Constructor Detail

ExtractSequences

public ExtractSequences()

Method Detail

requiresReference

protected boolean requiresReference()

Overrides:

requiresReference in class CommandLineProgram

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.