Package picard.vcf
Class GatherVcfs
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- picard.cmdline.CommandLineProgram
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- picard.vcf.GatherVcfs
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@DocumentedFeature public class GatherVcfs extends CommandLineProgram
Simple little class that combines multiple VCFs that have exactly the same set of samples and totally discrete sets of loci.
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Field Summary
Fields Modifier and Type Field Description List<String>
COMMENT
List<File>
INPUT
File
OUTPUT
boolean
REORDER_INPUT_BY_FIRST_VARIANT
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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 GatherVcfs()
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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.-
Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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OUTPUT
@Argument(shortName="O", doc="Output VCF file.") public File OUTPUT
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COMMENT
@Argument(doc="Comment(s) to include in the merged output file\'s header.", optional=true, shortName="CO") public List<String> COMMENT
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REORDER_INPUT_BY_FIRST_VARIANT
@Argument(doc="If \'true\' the program will reorder INPUT according to the genomic location of the first variant in each file. this is useful since the order of variants in each file in INPUT come from non overlapping regions but the order of the files in INPUT is untrusted.", optional=true, shortName="RI") public boolean REORDER_INPUT_BY_FIRST_VARIANT
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Method Detail
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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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