public class VCFStandardHeaderLines
extends java.lang.Object
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
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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
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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.
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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
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public static VCFHeader repairStandardHeaderLines(VCFHeader header)
header
- public static java.util.Set<java.lang.String> addStandardFormatLines(java.util.Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, java.util.Collection<java.lang.String> IDs)
IDs
- public static java.util.Set<java.lang.String> addStandardFormatLines(java.util.Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, java.lang.String... IDs)
headerLines
- throwErrorForMissing
- IDs
- addStandardFormatLines(java.util.Set, boolean, java.util.Collection)
public static VCFFormatHeaderLine getFormatLine(java.lang.String ID, boolean throwErrorForMissing)
ID
- throwErrorForMissing
- public static VCFFormatHeaderLine getFormatLine(java.lang.String ID)
ID
- public static java.util.Set<java.lang.String> addStandardInfoLines(java.util.Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, java.util.Collection<java.lang.String> IDs)
IDs
- public static java.util.Set<java.lang.String> addStandardInfoLines(java.util.Set<VCFHeaderLine> headerLines, boolean throwErrorForMissing, java.lang.String... IDs)
IDs
- addStandardFormatLines(java.util.Set, boolean, java.util.Collection)
public static VCFInfoHeaderLine getInfoLine(java.lang.String ID, boolean throwErrorForMissing)
ID
- throwErrorForMissing
- public static VCFInfoHeaderLine getInfoLine(java.lang.String ID)
ID
-