picard.vcf

Class VcfFormatConverter

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.VcfFormatConverter

public class VcfFormatConverter
extends CommandLineProgram

Converts an ASCII VCF file to a binary BCF or vice versa.

Author:

jgentry@broadinstitute.org

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
static htsjdk.samtools.util.Log	LOG
java.io.File	OUTPUT
java.lang.Boolean	REQUIRE_INDEX

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
VcfFormatConverter()

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[] argv)

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

LOG

public static final htsjdk.samtools.util.Log LOG

INPUT

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

OUTPUT

@Option(doc="The BCF or VCF output file name.",
        shortName="O")
public java.io.File OUTPUT

REQUIRE_INDEX

@Option(doc="Fail if an index is not available for the input VCF/BCF")
public java.lang.Boolean REQUIRE_INDEX

Constructor Detail

VcfFormatConverter

public VcfFormatConverter()

Method Detail

main

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

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.