picard.vcf

Class MakeSitesOnlyVcf

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.MakeSitesOnlyVcf

public class MakeSitesOnlyVcf
extends CommandLineProgram

Writes out a VCF that contains all the site-level information for all records in the input VCF and no per-sample information.

Field Summary

Fields

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

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
MakeSitesOnlyVcf()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args)

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

@Option(shortName="I",
        doc="Input VCF or BCF")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="Output VCF or BCF to emit without per-sample info.")
public java.io.File OUTPUT

SAMPLE

@Option(shortName="S",
        doc="Optionally one or more samples to retain when building the \'sites-only\' VCF.",
        optional=true)
public java.util.Set<java.lang.String> SAMPLE

Constructor Detail

MakeSitesOnlyVcf

public MakeSitesOnlyVcf()

Method Detail

main

public static void main(java.lang.String[] args)

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.