Package picard.vcf
Class SortVcf
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.vcf.SortVcf
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@DocumentedFeature public class SortVcf extends CommandLineProgram
Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate. Can accept an external dictionary. If no external dictionary is supplied, multiple inputs' headers must have the same sequence dictionaries
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Field Summary
Fields Modifier and Type Field Description List<File>
INPUT
File
OUTPUT
File
SEQUENCE_DICTIONARY
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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 SortVcf()
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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="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)") public List<File> INPUT
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OUTPUT
@Argument(shortName="O", doc="Output VCF to be written.") public File OUTPUT
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SEQUENCE_DICTIONARY
@Argument(shortName="SD", optional=true) public File SEQUENCE_DICTIONARY
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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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