Package htsjdk.variant.vcf

Class VCFStandardHeaderLines

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

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 oldHeader)	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 Details

VCFStandardHeaderLines

public VCFStandardHeaderLines()

Method Details

repairStandardHeaderLines

public static VCFHeader repairStandardHeaderLines(VCFHeader oldHeader)

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.