public class VCFStandardHeaderLines
extends java.lang.Object
INFOand
FORMATfields. Provides simple mechanisms for 1) registering standard lines, 2) looking them up, and 3) adding them to headers.
Constructor and Description |
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VCFStandardHeaderLines() |
Modifier and Type | Method and Description |
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static java.util.Set<java.lang.String> |
addStandardFormatLines(java.util.Set<VCFHeaderLine> headerLines,
boolean throwErrorForMissing,
java.util.Collection<java.lang.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 java.util.Set<java.lang.String> |
addStandardFormatLines(java.util.Set<VCFHeaderLine> headerLines,
boolean throwErrorForMissing,
java.lang.String... IDs) |
static java.util.Set<java.lang.String> |
addStandardInfoLines(java.util.Set<VCFHeaderLine> headerLines,
boolean throwErrorForMissing,
java.util.Collection<java.lang.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 java.util.Set<java.lang.String> |
addStandardInfoLines(java.util.Set<VCFHeaderLine> headerLines,
boolean throwErrorForMissing,
java.lang.String... IDs) |
static VCFFormatHeaderLine |
getFormatLine(java.lang.String ID)
Returns the standard format line for
ID . |
static VCFFormatHeaderLine |
getFormatLine(java.lang.String ID,
boolean throwErrorForMissing)
Returns the standard format line for
ID . |
static VCFInfoHeaderLine |
getInfoLine(java.lang.String ID)
Returns the standard info line for
ID . |
static VCFInfoHeaderLine |
getInfoLine(java.lang.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. |
public static VCFHeader repairStandardHeaderLines(VCFHeader header)
VCFHeader
with standard VCF header lines repaired as necessary.public static java.util.Set<java.lang.String> addStandardFormatLines(java.util.Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, java.util.Collection<java.lang.String> IDs)
IDs
without standard descriptions, unless throwErrorForMissing
is true, in which
case this situation results in a TribbleException
public static java.util.Set<java.lang.String> addStandardFormatLines(java.util.Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, java.lang.String... IDs)
public static VCFFormatHeaderLine getFormatLine(java.lang.String ID, boolean throwErrorForMissing)
ID
.
If none exists, return null or throw an exception, depending on throwErrorForMissing
.public static VCFFormatHeaderLine getFormatLine(java.lang.String ID)
ID
.
If none exists, throw an TribbleException
public static java.util.Set<java.lang.String> addStandardInfoLines(java.util.Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, java.util.Collection<java.lang.String> IDs)
IDs
to header, returning the set of
IDs without standard descriptions, unless throwErrorForMissing
is true, in which
case this situation results in a TribbleException
.public static java.util.Set<java.lang.String> addStandardInfoLines(java.util.Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, java.lang.String... IDs)
public static VCFInfoHeaderLine getInfoLine(java.lang.String ID, boolean throwErrorForMissing)
ID
.
If none exists, return null
or throw a TribbleException
, depending on throwErrorForMissing
.public static VCFInfoHeaderLine getInfoLine(java.lang.String ID)
ID
.
If none exists throw a TribbleException
.