VCF (groovy-ngs-utils API)

gngs.VCF

All Implemented Interfaces and Traits:

java.lang.Iterable
```
class VCF
extends java.lang.Object
```
The VCF class supports simple parsing, filtering, querying and updating of VCF files.
The primary method is the parse(Closure) method which can be optionally passed a file name, stream, or if left out, will parse from standard input. When a Closure is supplied, it can be used for filtering and updating the VCF file as it is read. Each record is passed to the closure as it is read, and if false is returned from the closure it will be discarded:
```
 // Let's find all the indels on chr10!
 vcf = VCF.parse('test.vcf') { v ->
   v.chr == 'chr10' && (v.type == 'INS' || v.type == 'DEL')
 }
 
```
Various forms of information can be queried - the INFO section is parsed to a map and genotype information is available, referred to as the "dosage" for each sample with respect to the variant (an integer number of copies, 0,1,2). Support for SnpEff and VEP annotations is also provided via dedicated properties that return a list of SnpEffInfo objects describing the various annotations available. See the Variant class for more information about individual variants.
Note that most information is lazily computed so the cost of parsing complex fields is deferred unless they are asked for.
Updating variants requires a special procedure because related fields need to be sycnhronised after modification, and it is a strong convention to add a header line describing updates. An update method provides a closure based mechanism to make this straight forward:
```
 v.update { v.info.FOO='bar' }
 
```
Limited support for "Pedigrees" is available. At the moment only grouping of samples into families is supported and intra-family relationships are not modeled.
The Iterable interface and "in" operator are supported, allowing all the normal Groovy collection-manipulation methods. For example, you can do common iteration and membership tests:
for(Variant v in vcf) { if(v in vcf2) { ... } } or grouping, counting, etc: vcf.countBy { it.chr } // Count of variants by chromosome
If your desire is to lookup a specific region in a very large VCF file, you should index the VCF file and use the VCFIndex class to query the region specifically.
To stream a VCF without storing in memory, use the filter(Closure) methods which will print output, including header, directly to the output.
Authors:
simon.sadedin@mcri.edu.au

Properties Summary

Properties
Type	Name and description
`static int`	`FORMAT_COLUMN_INDEX`
`static int`	`SAMPLE_COLUMN_INDEX`
`java.util.Map<java.lang.String, java.util.List<Variant>>`	`chrPosIndex`
`java.lang.String`	`fileName`
`java.util.Map<java.lang.String, java.util.List<Variant>>`	`genes` Index of variants by affected gene Note that a variant can affect more than one gene, so will appear multiple times in the value side of the map
`java.util.List<java.lang.String>`	`headerLines`
`java.lang.String[]`	`lastHeaderLine`
`boolean`	`lazyLoad`
`java.util.List<Pedigree>`	`pedigrees`
`java.util.List<Pedigree>`	`samplePedigrees`
`java.util.List<java.lang.String>`	`samples`
`java.util.List<Variant>`	`variants`

Constructor Summary

Constructors
Constructor and description
`VCF ()`
`VCF (File file)` Creates an empty VCF file based on the header of the given VCF file
`VCF (java.lang.String fileName)` Creates an empty VCF file based on the header of the given VCF file
`VCF (java.lang.Iterable<Variant> variants)` Creates a VCF containing all the VCFs, and initialised with the header from the first variant

Methods Summary

Methods
Type Params	Return Type	Name and description
	`VCF`	`add(Variant v)` Add the given variant to this VCF
	`void`	`addInfoHeader(java.lang.String id, java.lang.String desc, java.lang.Object value)` Add a header for describing an info value to be added to a VCF.
	`void`	`addInfoHeaders(java.util.List<java.lang.String> linesToAdd)` Add new INFO header fields to this VCF
	`java.lang.Object`	`asType(java.lang.Class clazz)`
	`java.lang.String`	`buildGtFieldValue(java.lang.String gt, java.util.List<java.lang.String> myGtFields, java.util.List<java.lang.String> includedFields)`
	`double`	`denovoRate(int proband, int parent1, int parent2)` Calculate the fraction of denovo variants if this VCF contains a trio with the indexes of the samples as given
	`double`	`denovoRate(VCF m, VCF d)`
	`void`	`each(Closure c)`
	`static void`	`filter(File f, Closure c = null)`
	`static void`	`filter(File f, java.util.List<Pedigree> peds, Closure c = null)`
	`static void`	`filter(java.lang.String fileName, Closure c = null)`
	`static void`	`filter(java.lang.String fileName, java.util.List<Pedigree> peds, Closure c = null)`
	`static void`	`filter(Closure c = null)`
	`static void`	`filter(Map options = [:], InputStream f, Closure c)`
	`static void`	`filter(Map options = [:], InputStream f, java.util.List<Pedigree> peds = null, Closure c = null)`
	`static VCF`	`filter(Map options, java.lang.String fileName, Closure c)`
	`static VCF`	`filter(Map options = [:], Reader r, Closure c)`
	`void`	`filterSamples(java.io.PrintStream p, java.util.List<java.lang.String> includeSamples)` Print out a version of this VCF with only the given samples included
	`Variant`	`find(Variant v)` Attempt to locate a variant having the same change as the given variant inside this VCF.
	`Pedigree`	`findPedigreeBySampleIndex(int i)`
	`java.util.Map<java.lang.String, java.lang.Integer>`	`getConsequenceCounts()` Calculate the number of variants for each different VEP consequence, returning a map of consequence => count.
	`java.util.List<java.lang.String>`	`getContigs()`
	`java.util.Map<java.lang.String, FormatMetaData>`	`getFormatMetaData()`
	`java.util.Map<java.lang.String, java.util.List<Variant>>`	`getGenes()`
	`java.util.List<Variant>`	`getHighQualityHets(VCF p2)` Finds a set of high quality SNPs that distinguish this VCF from the other VCF provided.
	`VCFIndex`	`getIndex()`
	`java.util.Map<java.lang.String, java.lang.Object>`	`getInfoMetaData(java.lang.String id)`
	`int`	`getSize()`
	`java.lang.String[]`	`getVepColumns()`
	`java.lang.String[]`	`getVepColumns(java.lang.String vepType)` Dedicated support for dynamically returning the VEP columns present in this VCF file
	`Sex`	`guessSex(java.lang.String sampleId, int sampleSize = 500)` Return the sex of a sample, estimated from the heterozygosity of its variants.
	`Sex`	`guessSex(int sampleIndex = 0, int sampleSize = 500)` Attempt to guess the sex of a human VCF file by sampling high quality variants on the X chromosome.
	`boolean`	`hasInfo(java.lang.String id)` Return true if this VCF file contains the specified INFO tags
	`boolean`	`isCase(java.lang.Object obj)` Support for the convenience syntax to check if a VCF contains a specific variant with the form: if(variant in vcf) { .... } Note however that dosage of the variant is NOT compared, so a variant is "in" a VCF even if its allele count / zygosity is different to the variant of interest.
	`java.util.Iterator<Variant>`	`iterator()`
	`VCF`	`load(Closure c = null)`
	`VCF`	`merge(VCF other)` Perform a simplistic (emphasis on simplistic) merge between VCFs.
	`static VCF`	`parse(java.lang.String fileName, Pedigrees peds, Closure c = null)`
	`static VCF`	`parse(Map options = [:], java.lang.String fileName, java.util.List<Pedigree> peds = null, Closure c = null)` Convenience method to accept string for parsing file
	`static VCF`	`parse(Map options = [:], java.lang.String fileName, Closure c)`
	`static VCF`	`parse(File f, java.util.List<Pedigree> peds = null, Closure c = null)`
	`static VCF`	`parse(Map options, File f, java.util.List<Pedigree> peds = null, Closure c = null)`
	`static VCF`	`parse(Closure c = null)`
	`static VCF`	`parse(java.util.List<Pedigree> peds, Closure c = null)`
	`static VCF`	`parse(InputStream f, java.util.List<Pedigree> peds = null, Closure c = null)`
	`static VCF`	`parse(Map options, InputStream f, java.util.List<Pedigree> peds = null, Closure c = null)`
	`static VCF`	`parse(Map options = [:], Reader r, boolean filterMode, Closure c)`
	`FormatMetaData`	`parseFormatMetaDataLine(java.lang.String line)`
	`java.util.Map<java.lang.String, java.lang.Object>`	`parseInfoMetaData(java.lang.String info)` Parse a VCF INFO meta data line and return the values as a Map
	`void`	`parseLastHeaderLine()` Extract sample names and other info from the final header line in the VCF file
	`java.util.Map<java.lang.String, java.lang.String>`	`parseVepColumns()`
	`void`	`print()`
	`void`	`print(PrintWriter p)`
	`void`	`print(java.lang.Appendable p)`
	`void`	`printHeader(java.lang.Appendable w)`
	`void`	`printHeader()`
	`static void`	`processParsedVariant(VCFParseContext ctx, Variant v)`
	`void`	`renameSample(java.lang.String fromId, java.lang.String toId)` Change the sample ids for this VCF
	`void`	`replaceSamples(java.util.List<java.lang.String> sampleIds)` Replace the sample ids in the VCF with the given ones
	`int`	`sampleIndex(java.lang.String sampleName)`
	`java.lang.String`	`sniffGenomeBuild()` Attempts to identify which version of human genome build this VCF was created from.
	`Regions`	`toBED()`
	`java.util.List<java.util.Map<java.lang.String, java.lang.Object>>`	`toListMap()`
	`Regions`	`toRegions()`
	`java.lang.String`	`toString()`
	`double`	`transmissionRate(VCF p1, VCF p2)` Calculate the rate at which variants are transmitted to this sample from p1, given p2 is the other parent.
	`Map`	`trioDenovoRate()` Infer proband and calculate rate of de novo variants for a VCF containing a trio.
	`java.util.List`	`variantsAt(java.lang.String chr, int pos)` Return a list of variants starting at the given location

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class java.lang.Object`	`java.lang.Object#wait(long, int), java.lang.Object#wait(long), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll()`

- Property Detail
  - static final int FORMAT_COLUMN_INDEX
  - static final int SAMPLE_COLUMN_INDEX
  - java.util.Map<java.lang.String, java.util.List<Variant>> chrPosIndex
  - java.lang.String fileName
  - java.util.Map<java.lang.String, java.util.List<Variant>> genes
    
    Index of variants by affected gene Note that a variant can affect more than one gene, so will appear multiple times in the value side of the map
  - java.util.List<java.lang.String> headerLines
  - java.lang.String[] lastHeaderLine
  - boolean lazyLoad
  - java.util.List<Pedigree> pedigrees
  - java.util.List<Pedigree> samplePedigrees
  - java.util.List<java.lang.String> samples
  - java.util.List<Variant> variants
- Constructor Detail
  - VCF()
  - VCF(File file)
    
    Creates an empty VCF file based on the header of the given VCF file
    The VCF is set to lazy mode which auto-loads the variants when some methods are called.
    Parameters:
    fileName
  - VCF(java.lang.String fileName)
    
    Creates an empty VCF file based on the header of the given VCF file
    The VCF is set to lazy mode which auto-loads the variants when some methods are called.
    Parameters:
    fileName
  - VCF(java.lang.Iterable<Variant> variants)
    
    Creates a VCF containing all the VCFs, and initialised with the header from the first variant
    Parameters:
    variants
- Method Detail
  - @groovy.transform.CompileStatic VCF add(Variant v)
    
    Add the given variant to this VCF
  - void addInfoHeader(java.lang.String id, java.lang.String desc, java.lang.Object value)
    
    Add a header for describing an info value to be added to a VCF.
    Parameters:
    id
    desc
    value - A prototype value to infer the type of value for the INFO field from.
  - void addInfoHeaders(java.util.List<java.lang.String> linesToAdd)
    
    Add new INFO header fields to this VCF
    Searches for the last position of the other INFO lines and inserts the new lines at that position. If there are no other INFO lines, inserts the new lines at the end of the headers
    Parameters:
    lines
  - java.lang.Object asType(java.lang.Class clazz)
  - @groovy.transform.CompileStatic java.lang.String buildGtFieldValue(java.lang.String gt, java.util.List<java.lang.String> myGtFields, java.util.List<java.lang.String> includedFields)
  - @groovy.transform.CompileStatic double denovoRate(int proband, int parent1, int parent2)
    
    Calculate the fraction of denovo variants if this VCF contains a trio with the indexes of the samples as given
    Parameters:
    proband - index in the samples array of the proband
    parent1 - index in the samples array of first parent
    parent2 - index in the samples array of second parent
    Returns:
  - double denovoRate(VCF m, VCF d)
  - @groovy.transform.CompileStatic void each(Closure c)
  - static void filter(File f, Closure c = null)
  - static void filter(File f, java.util.List<Pedigree> peds, Closure c = null)
  - static void filter(java.lang.String fileName, Closure c = null)
  - static void filter(java.lang.String fileName, java.util.List<Pedigree> peds, Closure c = null)
  - static void filter(Closure c = null)
  - static void filter(Map options = [:], InputStream f, Closure c)
  - static void filter(Map options = [:], InputStream f, java.util.List<Pedigree> peds = null, Closure c = null)
  - @groovy.transform.CompileStatic static VCF filter(Map options, java.lang.String fileName, Closure c)
  - @groovy.transform.CompileStatic static VCF filter(Map options = [:], Reader r, Closure c)
  - void filterSamples(java.io.PrintStream p, java.util.List<java.lang.String> includeSamples)
    
    Print out a version of this VCF with only the given samples included
  - @groovy.transform.CompileStatic Variant find(Variant v)
    
    Attempt to locate a variant having the same change as the given variant inside this VCF.
    This function does not guarantee to find the change, if it exists. Currently, it will only locate the change if it is represented by an entry in the VCF starting at the same reference position. A variant will be returned if any allele in the identified variant matches any allele in the given variant. These operations become much more reliable (but still not 100% reliable) when both VCFs from which the variants are drawn are decomposed into primitives.
    Parameters:
    v
    Returns:
    a Variant matching v, if one is found, otherwise null
  - Pedigree findPedigreeBySampleIndex(int i)
  - java.util.Map<java.lang.String, java.lang.Integer> getConsequenceCounts()
    
    Calculate the number of variants for each different VEP consequence, returning a map of consequence => count.
  - @groovy.transform.CompileStatic java.util.List<java.lang.String> getContigs()
  - java.util.Map<java.lang.String, FormatMetaData> getFormatMetaData()
  - @groovy.transform.CompileStatic java.util.Map<java.lang.String, java.util.List<Variant>> getGenes()
  - java.util.List<Variant> getHighQualityHets(VCF p2)
    
    Finds a set of high quality SNPs that distinguish this VCF from the other VCF provided.
  - VCFIndex getIndex()
  - @groovy.transform.CompileStatic java.util.Map<java.lang.String, java.lang.Object> getInfoMetaData(java.lang.String id)
  - int getSize()
  - java.lang.String[] getVepColumns()
  - java.lang.String[] getVepColumns(java.lang.String vepType)
    
    Dedicated support for dynamically returning the VEP columns present in this VCF file
    Returns:
  - Sex guessSex(java.lang.String sampleId, int sampleSize = 500)
    
    Return the sex of a sample, estimated from the heterozygosity of its variants.
    See guessSex(int) for details of the implementation.
    Parameters:
    sampleId
    Returns:
    estimated Sex of Sample
  - Sex guessSex(int sampleIndex = 0, int sampleSize = 500)
    
    Attempt to guess the sex of a human VCF file by sampling high quality variants on the X chromosome.
    With various checks and constraints, the main test is:
  - if the number of homozygotes > 2 * number of hets, then sex = FEMALE
  - else sex = MALE
  - if various checks fail (eg: less than 100 variants available), then this method may return Sex.UNKNOWN. Note: requires an indexed VCF file
    Parameters:
    vcf
    Returns:
    estimated Sex of sample
  - @groovy.transform.CompileStatic boolean hasInfo(java.lang.String id)
    
    Return true if this VCF file contains the specified INFO tags
    Note: it only checks if the tag is described in the header, not whether any variant in the VCF actually has the INFO tag. You still need to account that any given record may be missing the tag.
    Parameters:
    id - id of INFO tag to check for
    Returns:
    true iff an INFO meta data line of the VCF file describes this tag
  - @groovy.transform.CompileStatic boolean isCase(java.lang.Object obj)
    
    Support for the convenience syntax to check if a VCF contains a specific variant with the form:
```
 if(variant in vcf) {
     ....
 }
 
```
    Note however that dosage of the variant is NOT compared, so a variant is "in" a VCF even if its allele count / zygosity is different to the variant of interest.
    Parameters:
    obj
    Returns:
    true iff the object is a Variant and a variant with the same allele and position exists in this VCF
  - @java.lang.Override @groovy.transform.CompileStatic java.util.Iterator<Variant> iterator()
  - VCF load(Closure c = null)
  - VCF merge(VCF other)
    
    Perform a simplistic (emphasis on simplistic) merge between VCFs.
  - Only works if the genotype fields are identical
  - Only works if the variants are normalised (primitised) to 1 per line - unnormalised variants will produce unpredictable results
    Parameters:
    other
    Returns:
    A VCF containing all the variants from both VCFs with genotype information merged where the same variant is in both VCFs, and null genotype information when it is missing in one or both VCFs.
  - static VCF parse(java.lang.String fileName, Pedigrees peds, Closure c = null)
  - static VCF parse(Map options = [:], java.lang.String fileName, java.util.List<Pedigree> peds = null, Closure c = null)
    
    Convenience method to accept string for parsing file
  - static VCF parse(Map options = [:], java.lang.String fileName, Closure c)
  - static VCF parse(File f, java.util.List<Pedigree> peds = null, Closure c = null)
  - @groovy.transform.CompileStatic static VCF parse(Map options, File f, java.util.List<Pedigree> peds = null, Closure c = null)
  - static VCF parse(Closure c = null)
  - static VCF parse(java.util.List<Pedigree> peds, Closure c = null)
  - static VCF parse(InputStream f, java.util.List<Pedigree> peds = null, Closure c = null)
  - static VCF parse(Map options, InputStream f, java.util.List<Pedigree> peds = null, Closure c = null)
  - @groovy.transform.CompileStatic static VCF parse(Map options = [:], Reader r, boolean filterMode, Closure c)
  - FormatMetaData parseFormatMetaDataLine(java.lang.String line)
  - java.util.Map<java.lang.String, java.lang.Object> parseInfoMetaData(java.lang.String info)
    
    Parse a VCF INFO meta data line and return the values as a Map
    Parameters:
    info
    Returns:
    map containing entries: ID, Number, Type, Description
  - @groovy.transform.CompileStatic void parseLastHeaderLine()
    
    Extract sample names and other info from the final header line in the VCF file If samples are specified, the samples parsed will be limited to the given samples. The VCF header line will be modified so that any output will only include the given samples.
  - java.util.Map<java.lang.String, java.lang.String> parseVepColumns()
  - void print()
  - @groovy.transform.CompileStatic void print(PrintWriter p)
  - @groovy.transform.CompileStatic void print(java.lang.Appendable p)
  - void printHeader(java.lang.Appendable w)
  - void printHeader()
  - @groovy.transform.CompileStatic static void processParsedVariant(VCFParseContext ctx, Variant v)
  - void renameSample(java.lang.String fromId, java.lang.String toId)
    
    Change the sample ids for this VCF
    Parameters:
    sampleIds
  - void replaceSamples(java.util.List<java.lang.String> sampleIds)
    
    Replace the sample ids in the VCF with the given ones
    Parameters:
    sampleIds
  - @groovy.transform.CompileStatic int sampleIndex(java.lang.String sampleName)
  - @groovy.transform.CompileStatic java.lang.String sniffGenomeBuild()
    
    Attempts to identify which version of human genome build this VCF was created from. Not applicable to non-human genomes.
    Returns:
    hg19,hg18,GRCh37,GRCh38,hg38 or null if one of these is not identified
  - Regions toBED()
  - @groovy.transform.CompileStatic java.util.List<java.util.Map<java.lang.String, java.lang.Object>> toListMap()
  - Regions toRegions()
  - java.lang.String toString()
  - double transmissionRate(VCF p1, VCF p2)
    
    Calculate the rate at which variants are transmitted to this sample from p1, given p2 is the other parent.
    Parameters:
    parent1
    parent2
    Returns:
  - Map trioDenovoRate()
    
    Infer proband and calculate rate of de novo variants for a VCF containing a trio.
    Returns:
    Map in the form [proband: , denovoRate: , ratio: ]
  - @groovy.transform.CompileStatic java.util.List variantsAt(java.lang.String chr, int pos)
    
    Return a list of variants starting at the given location
    Parameters:
    chr
    pos
    Returns:

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation

[Groovy] Class VCF

Properties Summary

Constructor Summary

Methods Summary

Inherited Methods Summary

Property Detail

static final int FORMAT_COLUMN_INDEX

static final int SAMPLE_COLUMN_INDEX

java.util.Map<java.lang.String, java.util.List<Variant>> chrPosIndex

java.lang.String fileName

java.util.Map<java.lang.String, java.util.List<Variant>> genes

java.util.List<java.lang.String> headerLines

java.lang.String[] lastHeaderLine

boolean lazyLoad

java.util.List<Pedigree> pedigrees

java.util.List<Pedigree> samplePedigrees

java.util.List<java.lang.String> samples

java.util.List<Variant> variants

Constructor Detail

VCF()

VCF(File file)

VCF(java.lang.String fileName)

VCF(java.lang.Iterable<Variant> variants)

Method Detail

@groovy.transform.CompileStatic VCF add(Variant v)

void addInfoHeader(java.lang.String id, java.lang.String desc, java.lang.Object value)

void addInfoHeaders(java.util.List<java.lang.String> linesToAdd)

java.lang.Object asType(java.lang.Class clazz)

@groovy.transform.CompileStatic java.lang.String buildGtFieldValue(java.lang.String gt, java.util.List<java.lang.String> myGtFields, java.util.List<java.lang.String> includedFields)

@groovy.transform.CompileStatic double denovoRate(int proband, int parent1, int parent2)

double denovoRate(VCF m, VCF d)

@groovy.transform.CompileStatic void each(Closure c)

static void filter(File f, Closure c = null)

static void filter(File f, java.util.List<Pedigree> peds, Closure c = null)

static void filter(java.lang.String fileName, Closure c = null)

static void filter(java.lang.String fileName, java.util.List<Pedigree> peds, Closure c = null)

static void filter(Closure c = null)

static void filter(Map options = [:], InputStream f, Closure c)

static void filter(Map options = [:], InputStream f, java.util.List<Pedigree> peds = null, Closure c = null)

@groovy.transform.CompileStatic static VCF filter(Map options, java.lang.String fileName, Closure c)

@groovy.transform.CompileStatic static VCF filter(Map options = [:], Reader r, Closure c)

void filterSamples(java.io.PrintStream p, java.util.List<java.lang.String> includeSamples)

@groovy.transform.CompileStatic Variant find(Variant v)

Pedigree findPedigreeBySampleIndex(int i)

java.util.Map<java.lang.String, java.lang.Integer> getConsequenceCounts()

@groovy.transform.CompileStatic java.util.List<java.lang.String> getContigs()

java.util.Map<java.lang.String, FormatMetaData> getFormatMetaData()

@groovy.transform.CompileStatic java.util.Map<java.lang.String, java.util.List<Variant>> getGenes()

java.util.List<Variant> getHighQualityHets(VCF p2)

VCFIndex getIndex()

@groovy.transform.CompileStatic java.util.Map<java.lang.String, java.lang.Object> getInfoMetaData(java.lang.String id)

int getSize()

java.lang.String[] getVepColumns()

java.lang.String[] getVepColumns(java.lang.String vepType)

Sex guessSex(java.lang.String sampleId, int sampleSize = 500)

Sex guessSex(int sampleIndex = 0, int sampleSize = 500)

@groovy.transform.CompileStatic boolean hasInfo(java.lang.String id)

@groovy.transform.CompileStatic boolean isCase(java.lang.Object obj)

@java.lang.Override @groovy.transform.CompileStatic java.util.Iterator<Variant> iterator()

VCF load(Closure c = null)

VCF merge(VCF other)

static VCF parse(java.lang.String fileName, Pedigrees peds, Closure c = null)

static VCF parse(Map options = [:], java.lang.String fileName, java.util.List<Pedigree> peds = null, Closure c = null)

static VCF parse(Map options = [:], java.lang.String fileName, Closure c)

static VCF parse(File f, java.util.List<Pedigree> peds = null, Closure c = null)

@groovy.transform.CompileStatic static VCF parse(Map options, File f, java.util.List<Pedigree> peds = null, Closure c = null)

static VCF parse(Closure c = null)

static VCF parse(java.util.List<Pedigree> peds, Closure c = null)

static VCF parse(InputStream f, java.util.List<Pedigree> peds = null, Closure c = null)

static VCF parse(Map options, InputStream f, java.util.List<Pedigree> peds = null, Closure c = null)

@groovy.transform.CompileStatic static VCF parse(Map options = [:], Reader r, boolean filterMode, Closure c)

FormatMetaData parseFormatMetaDataLine(java.lang.String line)

java.util.Map<java.lang.String, java.lang.Object> parseInfoMetaData(java.lang.String info)

@groovy.transform.CompileStatic void parseLastHeaderLine()

java.util.Map<java.lang.String, java.lang.String> parseVepColumns()

void print()

@groovy.transform.CompileStatic void print(PrintWriter p)

@groovy.transform.CompileStatic void print(java.lang.Appendable p)

void printHeader(java.lang.Appendable w)

void printHeader()