java.lang.Object
- htsjdk.variant.vcf.VCFStandardHeaderLines

```
public class VCFStandardHeaderLines
extends Object
```
Manages header lines for standard VCF
```
INFO
```
and
```
FORMAT
```
fields. Provides simple mechanisms for 1) registering standard lines, 2) looking them up, and 3) adding them to headers.
Since:

6/12

Constructor Summary

Constructors
Constructor Description

VCFStandardHeaderLines()

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static Set<String>`	`addStandardFormatLines(Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, String... IDs)`
`static Set<String>`	`addStandardFormatLines(Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, Collection<String> IDs)`	Adds header lines for each of the format fields in IDs to header, returning the set of `IDs` without standard descriptions, unless `throwErrorForMissing` is true, in which case this situation results in a `TribbleException`
`static Set<String>`	`addStandardInfoLines(Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, String... IDs)`
`static Set<String>`	`addStandardInfoLines(Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, Collection<String> IDs)`	Adds header lines for each of the info fields in `IDs` to header, returning the set of IDs without standard descriptions, unless `throwErrorForMissing` is true, in which case this situation results in a `TribbleException`.
`static VCFFormatHeaderLine`	`getFormatLine(String ID)`	Returns the standard format line for `ID`.
`static VCFFormatHeaderLine`	`getFormatLine(String ID, boolean throwErrorForMissing)`	Returns the standard format line for `ID`.
`static VCFInfoHeaderLine`	`getInfoLine(String ID)`	Returns the standard info line for `ID`.
`static VCFInfoHeaderLine`	`getInfoLine(String ID, boolean throwErrorForMissing)`	Returns the standard info line for `ID`.
`static VCFHeader`	`repairStandardHeaderLines(VCFHeader header)`	Walks over the VCF header and repairs the standard VCF header lines in it, returning a freshly allocated `VCFHeader` with standard VCF header lines repaired as necessary.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail
- VCFStandardHeaderLines
```
public VCFStandardHeaderLines()
```

Method Detail

repairStandardHeaderLines
```
public static VCFHeader repairStandardHeaderLines(VCFHeader header)
```
Walks over the VCF header and repairs the standard VCF header lines in it, returning a freshly allocated VCFHeader with standard VCF header lines repaired as necessary.

addStandardFormatLines

public static Set<String> addStandardFormatLines(Set<VCFHeaderLine> headerLines,
                                                 boolean throwErrorForMissing,
                                                 Collection<String> IDs)

Adds header lines for each of the format fields in IDs to header, returning the set of IDs without standard descriptions, unless throwErrorForMissing is true, in which case this situation results in a TribbleException

addStandardFormatLines

public static Set<String> addStandardFormatLines(Set<VCFHeaderLine> headerLines,
                                                 boolean throwErrorForMissing,
                                                 String... IDs)

See Also:: addStandardFormatLines(java.util.Set, boolean, java.util.Collection)

getFormatLine

public static VCFFormatHeaderLine getFormatLine(String ID,
                                                boolean throwErrorForMissing)

Returns the standard format line for ID. If none exists, return null or throw an exception, depending on throwErrorForMissing.

getFormatLine
```
public static VCFFormatHeaderLine getFormatLine(String ID)
```
Returns the standard format line for ID. If none exists, throw an TribbleException

addStandardInfoLines

public static Set<String> addStandardInfoLines(Set<VCFHeaderLine> headerLines,
                                               boolean throwErrorForMissing,
                                               Collection<String> IDs)

Adds header lines for each of the info fields in IDs to header, returning the set of IDs without standard descriptions, unless throwErrorForMissing is true, in which case this situation results in a TribbleException.

addStandardInfoLines

public static Set<String> addStandardInfoLines(Set<VCFHeaderLine> headerLines,
                                               boolean throwErrorForMissing,
                                               String... IDs)

See Also:: addStandardFormatLines(java.util.Set, boolean, java.util.Collection)

getInfoLine

public static VCFInfoHeaderLine getInfoLine(String ID,
                                            boolean throwErrorForMissing)

Returns the standard info line for ID. If none exists, return null or throw a TribbleException, depending on throwErrorForMissing.

getInfoLine
```
public static VCFInfoHeaderLine getInfoLine(String ID)
```
Returns the standard info line for ID. If none exists throw a TribbleException.

Class VCFStandardHeaderLines

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

VCFStandardHeaderLines

Method Detail

repairStandardHeaderLines

addStandardFormatLines

addStandardFormatLines

getFormatLine

getFormatLine

addStandardInfoLines

addStandardInfoLines

getInfoLine

getInfoLine