Package picard.reference
Class ExtractSequences
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.reference.ExtractSequences
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@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.
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Field Summary
Fields Modifier and Type Field Description File
INTERVAL_LIST
int
LINE_LENGTH
File
OUTPUT
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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
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Constructor Summary
Constructors Constructor Description ExtractSequences()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.protected boolean
requiresReference()
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Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
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Field Detail
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INTERVAL_LIST
@Argument(doc="Interval list describing intervals to be extracted from the reference sequence.") public File INTERVAL_LIST
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OUTPUT
@Argument(shortName="O", doc="Output FASTA file.") public File OUTPUT
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LINE_LENGTH
@Argument(doc="Maximum line length for sequence data.") public int LINE_LENGTH
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Method Detail
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requiresReference
protected boolean requiresReference()
- Overrides:
requiresReference
in classCommandLineProgram
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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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