Package picard.vcf
Class GatherVcfs
java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.GatherVcfs
Simple little class that combines multiple VCFs that have exactly the same set of samples
and nonoverlapping sets of loci.
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Field Summary
FieldsFields 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, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
doWork()
Do the work after command line has been parsed.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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INPUT
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OUTPUT
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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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Constructor Details
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GatherVcfs
public GatherVcfs()
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Method Details
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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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