picard.vcf

Class MakeVcfSampleNameMap

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.MakeVcfSampleNameMap

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
 

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<java.lang.String>	INPUT
java.io.File	OUTPUT

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

Constructor Summary

Constructors

Constructor and Description
MakeVcfSampleNameMap()

Method Summary

Modifier and Type	Method and 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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT

@Argument(shortName="I",
          doc="One or more input VCFs to extract sample names from.",
          minElements=1)
public java.util.List<java.lang.String> INPUT

OUTPUT

@Argument(shortName="O",
          doc="Output file to write the sample-name map to.")
public java.io.File OUTPUT

Constructor Detail

MakeVcfSampleNameMap

public MakeVcfSampleNameMap()

Method Detail

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 class CommandLineProgram

Returns:

program exit status.