Package | Description |
---|---|
htsjdk.variant.bcf2 | |
htsjdk.variant.variantcontext | |
htsjdk.variant.variantcontext.writer | |
htsjdk.variant.vcf |
Modifier and Type | Field and Description |
---|---|
VCFHeader |
BCF2Codec.LazyData.header |
Modifier and Type | Method and Description |
---|---|
protected VCFHeader |
BCF2Codec.getHeader() |
Modifier and Type | Method and Description |
---|---|
static boolean |
BCF2Utils.headerLinesAreOrderedConsistently(VCFHeader outputHeader,
VCFHeader genotypesBlockHeader)
Are the elements and their order in the output and input headers consistent so that
we can write out the raw genotypes block without decoding and recoding it?
If the order of INFO, FILTER, or contrig elements in the output header is different than
in the input header we must decode the blocks using the input header and then recode them
based on the new output order.
|
static java.util.ArrayList<java.lang.String> |
BCF2Utils.makeDictionary(VCFHeader header)
Create a strings dictionary from the VCF header
The dictionary is an ordered list of common VCF identifers (FILTER, INFO, and FORMAT)
fields.
|
Constructor and Description |
---|
BCF2GenotypeFieldDecoders(VCFHeader header) |
LazyData(VCFHeader header,
int nGenotypeFields,
byte[] bytes) |
Modifier and Type | Method and Description |
---|---|
java.util.List<java.lang.String> |
VariantContext.calcVCFGenotypeKeys(VCFHeader header) |
VariantContext |
VariantContext.fullyDecode(VCFHeader header,
boolean lenientDecoding)
Return a VC equivalent to this one but where all fields are fully decoded
See VariantContext document about fully decoded
|
static VCFCompoundHeaderLine |
VariantContextUtils.getMetaDataForField(VCFHeader header,
java.lang.String field) |
Modifier and Type | Method and Description |
---|---|
protected VCFHeader |
BCF2FieldWriter.getHeader() |
Modifier and Type | Method and Description |
---|---|
void |
BCF2FieldWriterManager.setup(VCFHeader header,
BCF2Encoder encoder,
java.util.Map<java.lang.String,java.lang.Integer> stringDictionary)
Setup the FieldWriters appropriate to each INFO and FORMAT in the VCF header
Must be called before any of the getter methods will work
|
void |
VariantContextWriter.writeHeader(VCFHeader header) |
void |
AsyncVariantContextWriter.writeHeader(VCFHeader header) |
Constructor and Description |
---|
BCF2FieldWriter(VCFHeader header,
BCF2FieldEncoder fieldEncoder) |
FTGenotypesWriter(VCFHeader header,
BCF2FieldEncoder fieldEncoder) |
GenericSiteWriter(VCFHeader header,
BCF2FieldEncoder fieldEncoder) |
GenotypesWriter(VCFHeader header,
BCF2FieldEncoder fieldEncoder) |
GTWriter(VCFHeader header,
BCF2FieldEncoder fieldEncoder) |
IGFGenotypesWriter(VCFHeader header,
BCF2FieldEncoder fieldEncoder,
IntGenotypeFieldAccessors.Accessor ige) |
IntegerTypeGenotypesWriter(VCFHeader header,
BCF2FieldEncoder fieldEncoder) |
SiteWriter(VCFHeader header,
BCF2FieldEncoder fieldEncoder) |
StaticallyTypeGenotypesWriter(VCFHeader header,
BCF2FieldEncoder fieldEncoder) |
Modifier and Type | Field and Description |
---|---|
protected VCFHeader |
AbstractVCFCodec.header |
Modifier and Type | Method and Description |
---|---|
VCFHeader |
VCFFileReader.getFileHeader()
Returns the VCFHeader associated with this VCF/BCF file.
|
protected VCFHeader |
AbstractVCFCodec.parseHeaderFromLines(java.util.List<java.lang.String> headerStrings,
VCFHeaderVersion version)
create a VCF header from a set of header record lines
|
static VCFHeader |
VCFStandardHeaderLines.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
|
VCFHeader |
AbstractVCFCodec.setVCFHeader(VCFHeader header,
VCFHeaderVersion version)
Explicitly set the VCFHeader on this codec.
|
static VCFHeader |
VCFUtils.withUpdatedContigs(VCFHeader oldHeader,
java.io.File referenceFile,
SAMSequenceDictionary refDict)
Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary
|
Modifier and Type | Method and Description |
---|---|
static VCFHeader |
VCFStandardHeaderLines.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
|
void |
VCFEncoder.setVCFHeader(VCFHeader header)
Deprecated.
|
VCFHeader |
AbstractVCFCodec.setVCFHeader(VCFHeader header,
VCFHeaderVersion version)
Explicitly set the VCFHeader on this codec.
|
static VCFHeader |
VCFUtils.withUpdatedContigs(VCFHeader oldHeader,
java.io.File referenceFile,
SAMSequenceDictionary refDict)
Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary
|
Modifier and Type | Method and Description |
---|---|
static java.util.Set<VCFHeaderLine> |
VCFUtils.smartMergeHeaders(java.util.Collection<VCFHeader> headers,
boolean emitWarnings) |
Constructor and Description |
---|
VCFEncoder(VCFHeader header,
boolean allowMissingFieldsInHeader,
boolean outputTrailingFormatFields)
Prepare a VCFEncoder that will encode records appropriate to the given VCF header, optionally
allowing missing fields in the header.
|
VCFHeader(VCFHeader toCopy)
Creates a deep copy of the given VCFHeader, duplicating all its metadata and
sample names.
|
VCFRecordCodec(VCFHeader header) |
VCFRecordCodec(VCFHeader header,
boolean allowMissingFieldsInHeader) |