java.lang.Object
- htsjdk.tribble.AbstractFeatureCodec<T,LineIterator>
- - htsjdk.tribble.AsciiFeatureCodec<VariantContext>
  - - htsjdk.variant.vcf.AbstractVCFCodec

All Implemented Interfaces:

FeatureCodec<VariantContext,LineIterator>, NameAwareCodec

Direct Known Subclasses:

VCF3Codec, VCFCodec
```
public abstract class AbstractVCFCodec
extends AsciiFeatureCodec<VariantContext>
implements NameAwareCodec
```

Field Summary

Fields
Modifier and Type	Field	Description
`protected Map<String,List<Allele>>`	`alleleMap`
`protected boolean`	`doOnTheFlyModifications`	If true, then we'll magically fix up VCF headers on the fly when we read them in
`protected HashMap<String,List<String>>`	`filterHash`
`protected String[]`	`genotypeParts`
`protected VCFHeader`	`header`
`protected int`	`lineNo`
`protected String[]`	`locParts`
`static int`	`MAX_ALLELE_SIZE_BEFORE_WARNING`
`protected String`	`name`
`protected static int`	`NUM_STANDARD_FIELDS`
`protected String[]`	`parts`
`protected String`	`remappedSampleName`	If non-null, we will replace the sample name read from the VCF header with this sample name.
`protected Map<String,String>`	`stringCache`
`static boolean`	`validate`
`protected VCFHeaderVersion`	`version`
`protected boolean`	`warnedAboutNoEqualsForNonFlag`

Constructor Summary

Constructors
Modifier Constructor Description

protected AbstractVCFCodec()

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`static boolean`	`canDecodeFile(String potentialInput, String MAGIC_HEADER_LINE)`
`LazyGenotypesContext.LazyData`	`createGenotypeMap(String str, List<Allele> alleles, String chr, int pos)`	create a genotype map
`VariantContext`	`decode(String line)`	decode the line into a feature (VariantContext)
`Feature`	`decodeLoc(String line)`	the fast decode function
`void`	`disableOnTheFlyModifications()`	Forces all VCFCodecs to not perform any on the fly modifications to the VCF header of VCF records.
`protected void`	`generateException(String message)`
`protected static void`	`generateException(String message, int lineNo)`
`VCFAltHeaderLine`	`getAltHeaderLine(String headerLineString, VCFHeaderVersion sourceVersion)`	Create and return a VCFAltHeaderLine object from a header line string that conforms to the `sourceVersion`
`protected String`	`getCachedString(String str)`	Return a cached copy of the supplied string.
`VCFHeader`	`getHeader()`
`VCFMetaHeaderLine`	`getMetaHeaderLine(String headerLineString, VCFHeaderVersion sourceVersion)`	Create and return a VCFMetaHeaderLine object from a header line string that conforms to the `sourceVersion`
`String`	`getName()`	get the name of this codec
`VCFPedigreeHeaderLine`	`getPedigreeHeaderLine(String headerLineString, VCFHeaderVersion sourceVersion)`	Create and return a VCFPedigreeHeaderLine object from a header line string that conforms to the `sourceVersion`
`VCFSampleHeaderLine`	`getSampleHeaderLine(String headerLineString, VCFHeaderVersion sourceVersion)`	Create and return a VCFSampleHeaderLine object from a header line string that conforms to the `sourceVersion`
`TabixFormat`	`getTabixFormat()`	Define the tabix format for the feature, used for indexing.
`VCFHeaderVersion`	`getVersion()`
`protected static Allele`	`oneAllele(String index, List<Allele> alleles)`	create a an allele from an index and an array of alleles
`protected static List<Allele>`	`parseAlleles(String ref, String alts, int lineNo)`	parse out the alleles
`protected abstract List<String>`	`parseFilters(String filterString)`	parse the filter string, first checking to see if we already have parsed it in a previous attempt
`protected static List<Allele>`	`parseGenotypeAlleles(String GT, List<Allele> alleles, Map<String,List<Allele>> cache)`	parse genotype alleles from the genotype string
`protected VCFHeader`	`parseHeaderFromLines(List<String> headerStrings, VCFHeaderVersion version)`	create a VCF header from a set of header record lines
`protected static Double`	`parseQual(String qualString)`	parse out the qual value
`void`	`setName(String name)`	set the name of this codec
`void`	`setRemappedSampleName(String remappedSampleName)`	Replaces the sample name read from the VCF header with the remappedSampleName.
`VCFHeader`	`setVCFHeader(VCFHeader newHeader, VCFHeaderVersion newVersion)`	Explicitly set the VCFHeader on this codec.

Methods inherited from class htsjdk.tribble.AsciiFeatureCodec
close, decode, isDone, makeIndexableSourceFromStream, makeSourceFromStream, readActualHeader, readHeader

Methods inherited from class htsjdk.tribble.AbstractFeatureCodec
decodeLoc, getFeatureType

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.tribble.FeatureCodec
canDecode, getPathToDataFile

- Field Detail
  - MAX_ALLELE_SIZE_BEFORE_WARNING
```
public static final int MAX_ALLELE_SIZE_BEFORE_WARNING
```
  - NUM_STANDARD_FIELDS
```
protected static final int NUM_STANDARD_FIELDS
```
    See Also:
    
    Constant Field Values
  - header
```
protected VCFHeader header
```
  - version
```
protected VCFHeaderVersion version
```
  - alleleMap
```
protected Map<String,List<Allele>> alleleMap
```
  - validate
```
public static boolean validate
```
  - parts
```
protected String[] parts
```
  - genotypeParts
```
protected String[] genotypeParts
```
  - locParts
```
protected final String[] locParts
```
  - filterHash
```
protected HashMap<String,List<String>> filterHash
```
  - name
```
protected String name
```
  - lineNo
```
protected int lineNo
```
  - stringCache
```
protected Map<String,String> stringCache
```
  - warnedAboutNoEqualsForNonFlag
```
protected boolean warnedAboutNoEqualsForNonFlag
```
  - doOnTheFlyModifications
```
protected boolean doOnTheFlyModifications
```
    If true, then we'll magically fix up VCF headers on the fly when we read them in
  - remappedSampleName
```
protected String remappedSampleName
```
    If non-null, we will replace the sample name read from the VCF header with this sample name. This feature works only for single-sample VCFs.
- Constructor Detail
  - AbstractVCFCodec
```
protected AbstractVCFCodec()
```
- Method Detail
  - parseFilters
```
protected abstract List<String> parseFilters(String filterString)
```
    parse the filter string, first checking to see if we already have parsed it in a previous attempt
    
    Parameters:
    
    filterString - the string to parse
    
    Returns:
    
    a set of the filters applied
  - parseHeaderFromLines
```
protected VCFHeader parseHeaderFromLines(List<String> headerStrings,
                                         VCFHeaderVersion version)
```
    create a VCF header from a set of header record lines
    
    Parameters:
    
    headerStrings - a list of strings that represent all the ## and # entries
    
    Returns:
    
    a VCFHeader object
  - getHeader
```
public VCFHeader getHeader()
```
    Returns:
    
    the header that was either explicitly set on this codec, or read from the file. May be null. The returned value should not be modified.
  - getVersion
```
public VCFHeaderVersion getVersion()
```
    Returns:
    
    the version number that was either explicitly set on this codec, or read from the file. May be null.
  - setVCFHeader
```
public VCFHeader setVCFHeader(VCFHeader newHeader,
                              VCFHeaderVersion newVersion)
```
    Explicitly set the VCFHeader on this codec. This will overwrite the header read from the file and the version state stored in this instance; conversely, reading the header from a file will overwrite whatever is set here.
    
    Parameters:
    
    newHeader -
    
    newVersion -
    
    Returns:
    
    the actual header for this codec. The returned header may not be identical to the header argument since the header lines may be "repaired" (i.e., rewritten) if doOnTheFlyModifications is set.
    
    Throws:
    
    TribbleException - if the requested header version is not compatible with the existing version
  - getAltHeaderLine
```
public VCFAltHeaderLine getAltHeaderLine(String headerLineString,
                                         VCFHeaderVersion sourceVersion)
```
    Create and return a VCFAltHeaderLine object from a header line string that conforms to the sourceVersion
    
    Parameters:
    
    headerLineString - VCF header line being parsed without the leading "##ALT="
    
    sourceVersion - the VCF header version derived from which the source was retrieved. The resulting header line object should be validate for this header version.
    
    Returns:
    
    a VCFAltHeaderLine object
  - getPedigreeHeaderLine
```
public VCFPedigreeHeaderLine getPedigreeHeaderLine(String headerLineString,
                                                   VCFHeaderVersion sourceVersion)
```
    Create and return a VCFPedigreeHeaderLine object from a header line string that conforms to the sourceVersion
    
    Parameters:
    
    headerLineString - VCF header line being parsed without the leading "##PEDIGREE="
    
    sourceVersion - the VCF header version derived from which the source was retrieved. The resulting header line object should be validate for this header version.
    
    Returns:
    
    a VCFPedigreeHeaderLine object
  - getMetaHeaderLine
```
public VCFMetaHeaderLine getMetaHeaderLine(String headerLineString,
                                           VCFHeaderVersion sourceVersion)
```
    Create and return a VCFMetaHeaderLine object from a header line string that conforms to the sourceVersion
    
    Parameters:
    
    headerLineString - VCF header line being parsed without the leading "##META="
    
    sourceVersion - the VCF header version derived from which the source was retrieved. The resulting header line object should be validate for this header version.
    
    Returns:
    
    a VCFMetaHeaderLine object
  - getSampleHeaderLine
```
public VCFSampleHeaderLine getSampleHeaderLine(String headerLineString,
                                               VCFHeaderVersion sourceVersion)
```
    Create and return a VCFSampleHeaderLine object from a header line string that conforms to the sourceVersion
    
    Parameters:
    
    headerLineString - VCF header line being parsed without the leading "##SAMPLE="
    
    sourceVersion - the VCF header version derived from which the source was retrieved. The resulting header line object should be validate for this header version.
    
    Returns:
    
    a VCFSampleHeaderLine object
  - decodeLoc
```
public Feature decodeLoc(String line)
```
    the fast decode function
    
    Parameters:
    
    line - the line of text for the record
    
    Returns:
    
    a feature, (not guaranteed complete) that has the correct start and stop
  - decode
```
public VariantContext decode(String line)
```
    decode the line into a feature (VariantContext)
    
    Specified by:
    
    decode in class AsciiFeatureCodec<VariantContext>
    
    Parameters:
    
    line - the line
    
    Returns:
    
    a VariantContext
    
    See Also:
    
    AsciiFeatureCodec.decode(htsjdk.tribble.readers.LineIterator)
  - getName
```
public String getName()
```
    get the name of this codec
    
    Specified by:
    
    getName in interface NameAwareCodec
    
    Returns:
    
    our set name
  - setName
```
public void setName(String name)
```
    set the name of this codec
    
    Specified by:
    
    setName in interface NameAwareCodec
    
    Parameters:
    
    name - new name
  - getCachedString
```
protected String getCachedString(String str)
```
    Return a cached copy of the supplied string.
    
    Parameters:
    
    str - string
    
    Returns:
    
    interned string
  - oneAllele
```
protected static Allele oneAllele(String index,
                                  List<Allele> alleles)
```
    create a an allele from an index and an array of alleles
    
    Parameters:
    
    index - the index
    
    alleles - the alleles
    
    Returns:
    
    an Allele
  - parseGenotypeAlleles
```
protected static List<Allele> parseGenotypeAlleles(String GT,
                                                   List<Allele> alleles,
                                                   Map<String,List<Allele>> cache)
```
    parse genotype alleles from the genotype string
    
    Parameters:
    
    GT - GT string
    
    alleles - list of possible alleles
    
    cache - cache of alleles for GT
    
    Returns:
    
    the allele list for the GT string
  - parseQual
```
protected static Double parseQual(String qualString)
```
    parse out the qual value
    
    Parameters:
    
    qualString - the quality string
    
    Returns:
    
    return a double
  - parseAlleles
```
protected static List<Allele> parseAlleles(String ref,
                                           String alts,
                                           int lineNo)
```
    parse out the alleles
    
    Parameters:
    
    ref - the reference base
    
    alts - a string of alternates to break into alleles
    
    lineNo - the line number for this record
    
    Returns:
    
    a list of alleles, and a pair of the shortest and longest sequence
  - canDecodeFile
```
public static boolean canDecodeFile(String potentialInput,
                                    String MAGIC_HEADER_LINE)
```
  - createGenotypeMap
```
public LazyGenotypesContext.LazyData createGenotypeMap(String str,
                                                       List<Allele> alleles,
                                                       String chr,
                                                       int pos)
```
    create a genotype map
    
    Parameters:
    
    str - the string
    
    alleles - the list of alleles
    
    Returns:
    
    a mapping of sample name to genotype object
  - disableOnTheFlyModifications
```
public final void disableOnTheFlyModifications()
```
    Forces all VCFCodecs to not perform any on the fly modifications to the VCF header of VCF records. Useful primarily for raw comparisons such as when comparing raw VCF records
  - setRemappedSampleName
```
public void setRemappedSampleName(String remappedSampleName)
```
    Replaces the sample name read from the VCF header with the remappedSampleName. Works only for single-sample VCFs -- attempting to perform sample name remapping for multi-sample VCFs will produce an Exception.
    
    Parameters:
    
    remappedSampleName - replacement sample name for the sample specified in the VCF header
  - generateException
```
protected void generateException(String message)
```
  - generateException
```
protected static void generateException(String message,
                                        int lineNo)
```
  - getTabixFormat
```
public TabixFormat getTabixFormat()
```
    Description copied from interface: FeatureCodec
    
    Define the tabix format for the feature, used for indexing. Default implementation throws an exception. Note that only AsciiFeatureCodec could read tabix files as defined in AbstractFeatureReader.getFeatureReader(String, String, FeatureCodec, boolean, java.util.function.Function, java.util.function.Function)
    
    Specified by:
    
    getTabixFormat in interface FeatureCodec<VariantContext,LineIterator>
    
    Returns:
    
    the format to use with tabix

Class AbstractVCFCodec

Field Summary

Constructor Summary

Method Summary

Methods inherited from class htsjdk.tribble.AsciiFeatureCodec

Methods inherited from class htsjdk.tribble.AbstractFeatureCodec

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.tribble.FeatureCodec

Field Detail

MAX_ALLELE_SIZE_BEFORE_WARNING

NUM_STANDARD_FIELDS

header

version

alleleMap

validate

parts

genotypeParts

locParts

filterHash

name

lineNo

stringCache

warnedAboutNoEqualsForNonFlag

doOnTheFlyModifications

remappedSampleName

Constructor Detail

AbstractVCFCodec

Method Detail

parseFilters

parseHeaderFromLines

getHeader

getVersion

setVCFHeader

getAltHeaderLine

getPedigreeHeaderLine

getMetaHeaderLine

getSampleHeaderLine

decodeLoc

decode

getName

setName

getCachedString

oneAllele

parseGenotypeAlleles

parseQual

parseAlleles

canDecodeFile

createGenotypeMap

disableOnTheFlyModifications

setRemappedSampleName

generateException

generateException

getTabixFormat