public class VCFHeader
extends java.lang.Object
implements java.io.Serializable
Modifier and Type | Class and Description |
---|---|
static class |
VCFHeader.HEADER_FIELDS |
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
CONTIG_KEY |
static java.lang.String |
EXCLUDE_INTERVALS_KEY |
static java.lang.String |
HEADER_INDICATOR |
static java.lang.String |
INTERVAL_MERGING_KEY |
static java.lang.String |
INTERVAL_PADDING_KEY |
static java.lang.String |
INTERVAL_SET_RULE_KEY |
static java.lang.String |
INTERVALS_KEY |
static java.lang.String |
METADATA_INDICATOR |
static java.lang.String |
REFERENCE_KEY |
static long |
serialVersionUID |
static java.lang.String |
SOURCE_KEY |
Constructor and Description |
---|
VCFHeader()
Create an empty VCF header with no header lines and no samples
|
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
|
VCFHeader(VCFHeader toCopy)
Creates a deep copy of the given VCFHeader, duplicating all its metadata and
sample names.
|
Modifier and Type | Method and Description |
---|---|
void |
addMetaDataLine(VCFHeaderLine headerLine)
Adds a new line to the VCFHeader.
|
int |
getColumnCount() |
java.util.List<VCFContigHeaderLine> |
getContigLines() |
VCFFilterHeaderLine |
getFilterHeaderLine(java.lang.String id) |
java.util.List<VCFFilterHeaderLine> |
getFilterLines() |
VCFFormatHeaderLine |
getFormatHeaderLine(java.lang.String id) |
java.util.Collection<VCFFormatHeaderLine> |
getFormatHeaderLines()
Returns the FORMAT HeaderLines in their original ordering
|
java.util.List<java.lang.String> |
getGenotypeSamples()
get the genotyping sample names
|
java.util.Set<VCFHeader.HEADER_FIELDS> |
getHeaderFields()
get the header fields in order they're presented in the input file (which is now required to be
the order presented in the spec).
|
java.util.List<VCFIDHeaderLine> |
getIDHeaderLines() |
VCFInfoHeaderLine |
getInfoHeaderLine(java.lang.String id) |
java.util.Collection<VCFInfoHeaderLine> |
getInfoHeaderLines()
Returns the INFO HeaderLines in their original ordering
|
java.util.Set<VCFHeaderLine> |
getMetaDataInInputOrder()
get the meta data, associated with this header, in sorted order
|
java.util.Set<VCFHeaderLine> |
getMetaDataInSortedOrder() |
VCFHeaderLine |
getMetaDataLine(java.lang.String key)
Get the VCFHeaderLine whose key equals key.
|
int |
getNGenotypeSamples() |
VCFHeaderLine |
getOtherHeaderLine(java.lang.String key) |
java.util.Collection<VCFHeaderLine> |
getOtherHeaderLines()
Returns the other HeaderLines in their original ordering
|
java.util.ArrayList<java.lang.String> |
getSampleNamesInOrder() |
java.util.HashMap<java.lang.String,java.lang.Integer> |
getSampleNameToOffset() |
SAMSequenceDictionary |
getSequenceDictionary()
Returns the contigs in this VCF file as a SAMSequenceDictionary.
|
VariantContextComparator |
getVCFRecordComparator() |
boolean |
hasFilterLine(java.lang.String id) |
boolean |
hasFormatLine(java.lang.String id) |
boolean |
hasGenotypingData()
do we have genotyping data?
|
boolean |
hasInfoLine(java.lang.String id) |
boolean |
isWriteCommandLine()
If true, and isWriteEngineHeaders also returns true, the command line will be written to the VCF.
|
boolean |
isWriteEngineHeaders()
If true additional engine headers will be written to the VCF, otherwise only the walker headers will be output.
|
boolean |
samplesWereAlreadySorted()
were the input samples sorted originally?
|
void |
setSequenceDictionary(SAMSequenceDictionary dictionary)
Completely replaces the contig records in this header with those in the given SAMSequenceDictionary.
|
void |
setWriteCommandLine(boolean writeCommandLine)
If true, and isWriteEngineHeaders also returns true, the command line will be written to the VCF.
|
void |
setWriteEngineHeaders(boolean writeEngineHeaders)
If true additional engine headers will be written to the VCF, otherwise only the walker headers will be output.
|
java.lang.String |
toString() |
public static final long serialVersionUID
public static final java.lang.String METADATA_INDICATOR
public static final java.lang.String HEADER_INDICATOR
public static final java.lang.String SOURCE_KEY
public static final java.lang.String REFERENCE_KEY
public static final java.lang.String CONTIG_KEY
public static final java.lang.String INTERVALS_KEY
public static final java.lang.String EXCLUDE_INTERVALS_KEY
public static final java.lang.String INTERVAL_MERGING_KEY
public static final java.lang.String INTERVAL_SET_RULE_KEY
public static final java.lang.String INTERVAL_PADDING_KEY
public VCFHeader()
public VCFHeader(java.util.Set<VCFHeaderLine> metaData)
metaData
- the meta data associated with this headerpublic VCFHeader(VCFHeader toCopy)
public VCFHeader(java.util.Set<VCFHeaderLine> metaData, java.util.Set<java.lang.String> genotypeSampleNames)
metaData
- the meta data associated with this headergenotypeSampleNames
- the sample namespublic VCFHeader(java.util.Set<VCFHeaderLine> metaData, java.util.List<java.lang.String> genotypeSampleNames)
public void addMetaDataLine(VCFHeaderLine headerLine)
headerLine
- header line to attempt to addpublic java.util.List<VCFContigHeaderLine> getContigLines()
public SAMSequenceDictionary getSequenceDictionary()
public void setSequenceDictionary(SAMSequenceDictionary dictionary)
public VariantContextComparator getVCFRecordComparator()
public java.util.List<VCFFilterHeaderLine> getFilterLines()
public java.util.List<VCFIDHeaderLine> getIDHeaderLines()
public java.util.Set<VCFHeader.HEADER_FIELDS> getHeaderFields()
public java.util.Set<VCFHeaderLine> getMetaDataInInputOrder()
public java.util.Set<VCFHeaderLine> getMetaDataInSortedOrder()
public VCFHeaderLine getMetaDataLine(java.lang.String key)
key
- public java.util.List<java.lang.String> getGenotypeSamples()
public int getNGenotypeSamples()
public boolean hasGenotypingData()
public boolean samplesWereAlreadySorted()
public int getColumnCount()
public java.util.Collection<VCFInfoHeaderLine> getInfoHeaderLines()
public java.util.Collection<VCFFormatHeaderLine> getFormatHeaderLines()
public VCFInfoHeaderLine getInfoHeaderLine(java.lang.String id)
id
- the header key namepublic VCFFormatHeaderLine getFormatHeaderLine(java.lang.String id)
id
- the header key namepublic VCFFilterHeaderLine getFilterHeaderLine(java.lang.String id)
id
- the header key namepublic boolean hasInfoLine(java.lang.String id)
public boolean hasFormatLine(java.lang.String id)
public boolean hasFilterLine(java.lang.String id)
public VCFHeaderLine getOtherHeaderLine(java.lang.String key)
key
- the header key namepublic java.util.Collection<VCFHeaderLine> getOtherHeaderLines()
public boolean isWriteEngineHeaders()
public void setWriteEngineHeaders(boolean writeEngineHeaders)
writeEngineHeaders
- true if additional engine headers will be written to the VCFpublic boolean isWriteCommandLine()
public void setWriteCommandLine(boolean writeCommandLine)
writeCommandLine
- true if the command line will be written to the VCFpublic java.util.ArrayList<java.lang.String> getSampleNamesInOrder()
public java.util.HashMap<java.lang.String,java.lang.Integer> getSampleNameToOffset()
public java.lang.String toString()
toString
in class java.lang.Object