picard.vcf

Class FixVcfHeader

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.FixVcfHeader

@DocumentedFeature
public class FixVcfHeader
extends CommandLineProgram

Tool for replacing or fixing up a VCF header.

Field Summary

Fields

Modifier and Type	Field and Description
int	CHECK_FIRST_N_RECORDS
boolean	ENFORCE_SAME_SAMPLES
java.io.File	HEADER
java.io.File	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
FixVcfHeader()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected int	doWork() Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

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="The input VCF/BCF file.")
public java.io.File INPUT

OUTPUT

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

CHECK_FIRST_N_RECORDS

@Argument(shortName="N",
          doc="Check only the first N records when searching for missing INFO and FORMAT fields.",
          optional=true)
public int CHECK_FIRST_N_RECORDS

HEADER

@Argument(shortName="H",
          doc="The replacement VCF header.",
          optional=true)
public java.io.File HEADER

ENFORCE_SAME_SAMPLES

@Argument(doc="Enforce that the samples are the same (and in the same order) when replacing the VCF header.",
          optional=true)
public boolean ENFORCE_SAME_SAMPLES

Constructor Detail

FixVcfHeader

public FixVcfHeader()

Method Detail

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

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.