Package picard.vcf
Class MakeVcfSampleNameMap
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.vcf.MakeVcfSampleNameMap
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public class MakeVcfSampleNameMap extends CommandLineProgram
Creates a TSV from sample name to VCF/GVCF path, with one line per input.Summary
Creates a TSV from sample name to VCF/GVCF path, with one line per input. Input VCF/GVCFs must contain a header describing exactly one sample.
Usage example:
java -jar picard.jar MakeVcfSampleNameMap \ INPUT=sample1.vcf.gz \ INPUT=sample2.vcf.gz \ OUTPUT=cohort.sample_map
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Field Summary
Fields Modifier and Type Field Description List<String>
INPUT
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 MakeVcfSampleNameMap()
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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, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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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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