Package | Description |
---|---|
htsjdk.variant.vcf |
Modifier and Type | Class and Description |
---|---|
class |
VCFCompoundHeaderLine
a base class for compound header lines, which include info lines and format lines (so far)
|
class |
VCFContigHeaderLine
A special class representing a contig VCF header line.
|
class |
VCFFilterHeaderLine |
class |
VCFFormatHeaderLine |
class |
VCFInfoHeaderLine |
class |
VCFSimpleHeaderLine |
Modifier and Type | Method and Description |
---|---|
VCFHeaderLine |
VCFHeader.getMetaDataLine(java.lang.String key)
Get the VCFHeaderLine whose key equals key.
|
VCFHeaderLine |
VCFHeader.getOtherHeaderLine(java.lang.String key) |
Modifier and Type | Method and Description |
---|---|
java.util.Set<VCFHeaderLine> |
VCFHeader.getMetaDataInInputOrder()
get the meta data, associated with this header, in sorted order
|
java.util.Set<VCFHeaderLine> |
VCFHeader.getMetaDataInSortedOrder() |
java.util.Collection<VCFHeaderLine> |
VCFHeader.getOtherHeaderLines()
Returns the other HeaderLines in their original ordering
|
static java.util.Set<VCFHeaderLine> |
VCFUtils.smartMergeHeaders(java.util.Collection<VCFHeader> headers,
boolean emitWarnings) |
static java.util.Set<VCFHeaderLine> |
VCFUtils.withUpdatedContigsAsLines(java.util.Set<VCFHeaderLine> oldLines,
java.io.File referenceFile,
SAMSequenceDictionary refDict) |
static java.util.Set<VCFHeaderLine> |
VCFUtils.withUpdatedContigsAsLines(java.util.Set<VCFHeaderLine> oldLines,
java.io.File referenceFile,
SAMSequenceDictionary refDict,
boolean referenceNameOnly) |
Modifier and Type | Method and Description |
---|---|
void |
VCFHeader.addMetaDataLine(VCFHeaderLine headerLine)
Adds a new line to the VCFHeader.
|
Modifier and Type | Method and Description |
---|---|
static java.util.Set<java.lang.String> |
VCFStandardHeaderLines.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> |
VCFStandardHeaderLines.addStandardFormatLines(java.util.Set<VCFHeaderLine> headerLines,
boolean throwErrorForMissing,
java.lang.String... IDs) |
static java.util.Set<java.lang.String> |
VCFStandardHeaderLines.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> |
VCFStandardHeaderLines.addStandardInfoLines(java.util.Set<VCFHeaderLine> headerLines,
boolean throwErrorForMissing,
java.lang.String... IDs) |
static java.util.Set<VCFHeaderLine> |
VCFUtils.withUpdatedContigsAsLines(java.util.Set<VCFHeaderLine> oldLines,
java.io.File referenceFile,
SAMSequenceDictionary refDict) |
static java.util.Set<VCFHeaderLine> |
VCFUtils.withUpdatedContigsAsLines(java.util.Set<VCFHeaderLine> oldLines,
java.io.File referenceFile,
SAMSequenceDictionary refDict,
boolean referenceNameOnly) |
Constructor and Description |
---|
VCFHeader(java.util.Set<VCFHeaderLine> metaData)
create a VCF header, given a list of meta data and auxiliary tags
|
VCFHeader(java.util.Set<VCFHeaderLine> metaData,
java.util.List<java.lang.String> genotypeSampleNames) |
VCFHeader(java.util.Set<VCFHeaderLine> metaData,
java.util.Set<java.lang.String> genotypeSampleNames)
create a VCF header, given a list of meta data and auxillary tags
|