FixVcfHeader (picard 2.18.2 API)

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 Description

int CHECK_FIRST_N_RECORDS

boolean ENFORCE_SAME_SAMPLES

File HEADER

File INPUT

File OUTPUT
- Fields inherited from class picard.cmdline.CommandLineProgram
  COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Fields
Modifier and Type	Field	Description
`int`	`CHECK_FIRST_N_RECORDS`
`boolean`	`ENFORCE_SAME_SAMPLES`
`File`	`HEADER`
`File`	`INPUT`
`File`	`OUTPUT`

Constructor Summary

Constructors
Constructor Description

FixVcfHeader()

Constructors
Constructor	Description
`FixVcfHeader()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected 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.
`static void`	`main(String[] args)`

Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, 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 File INPUT
```
  - OUTPUT
```
@Argument(shortName="O",
          doc="The output VCF/BCF file.")
public 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 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
  - main
```
public static void main(String[] args)
```
  - customCommandLineValidation
```
protected 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.

Class FixVcfHeader

Field Summary

Fields inherited from class picard.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

INPUT

OUTPUT

CHECK_FIRST_N_RECORDS

HEADER

ENFORCE_SAME_SAMPLES

Constructor Detail

FixVcfHeader

Method Detail

main

customCommandLineValidation

doWork