VcfHeader

java.lang.Object
- vcf.VcfHeader

```
public final class VcfHeader
extends java.lang.Object
```
Class VcfHeader represents the Variant Call Format (VCF) meta-information lines and the Variant Call Format header line that precede the first Variant Call Format record.

Instances of class VcfHeader are immutable.

Field Summary

Fields
Modifier and Type Field and Description

static java.lang.String HEADER_PREFIX
A string equal to the first nine tab-delimited fields of a VCF header line that contains sample data.

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`HEADER_PREFIX` A string equal to the first nine tab-delimited fields of a VCF header line that contains sample data.

Constructor Summary

Constructors
Constructor and Description
`VcfHeader(FileIt<java.lang.String> it)` Constructs a new `VcfHeader` object from the VCF meta-information lines and the VCF header line returned by the specified `FileIterator<String>`.
`VcfHeader(FileIt<java.lang.String> it, Filter<java.lang.String> sampleFilter)` Constructs a new `VcfHeader` object from the VCF meta-information lines and the VCF header line returned by the specified `FileIterator<String>`.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.io.File`	`file()` Returns the file from which data are read, or returns `null` if the source is standard input.
`java.lang.String`	`headerLine()` Returns the VCF header line.
`VcfMetaInfo`	`metaInfoLine(int index)` Returns the specified VCF meta-information line.
`int`	`nHeaderFields()` Returns the number of fields in the VCF header line before sample exclusions.
`int`	`nMetaInfoLines()` Returns the number of VCF meta-information lines.
`int`	`nSamples()` Returns the number of samples after sample exclusions.
`int`	`nUnfilteredSamples()` Returns the number of samples before sample exclusions.
`java.lang.String[]`	`sampleIds()` Returns `this.sample().ids()`.
`Samples`	`samples()` Return the list of samples after sample exclusions.
`java.lang.String`	`toString()` Returns the VCF meta-information lines and the VCF header line used to construct `this`.
`int`	`unfilteredSampleIndex(int sample)` Returns the index of the specified sample in the the list original list of samples before sample exclusions.

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

- Field Detail
  - HEADER_PREFIX
```
public static final java.lang.String HEADER_PREFIX
```
    A string equal to the first nine tab-delimited fields of a VCF header line that contains sample data.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - VcfHeader
```
public VcfHeader(FileIt<java.lang.String> it)
```
    Constructs a new VcfHeader object from the VCF meta-information lines and the VCF header line returned by the specified FileIterator<String>. This constructor will advance the FileIterator<String> to the point before the first VCF record in the file. The VcfHeader object will have no excluded samples.
    
    Parameters:
    
    it - an iterator that returns lines of VCF file
    
    Throws:
    
    java.lang.IllegalArgumentException - if any of the meta-information lines returned by the specified FileIterator<String> does not conform to the VCF specification
    
    java.lang.IllegalArgumentException - if the header lines returned by the specified FileIterator<String> does not conform to the VCF specification
    
    java.lang.IllegalArgumentException - if no header line is returned by the specified FileIterator<String>
    
    java.lang.NullPointerException - if it == null
  - VcfHeader
```
public VcfHeader(FileIt<java.lang.String> it,
                 Filter<java.lang.String> sampleFilter)
```
    Constructs a new VcfHeader object from the VCF meta-information lines and the VCF header line returned by the specified FileIterator<String>. This constructor will advance the FileIterator<String> to the point before the first VCF record in the file.
    
    Parameters:
    
    it - an iterator that returns lines of a VCF file
    
    sampleFilter - a sample filter or null
    
    Throws:
    
    java.lang.IllegalArgumentException - if any of the meta-information lines returned by the specified FileIterator<String> does not conform to the VCF specification
    
    java.lang.IllegalArgumentException - if the header lines returned by the specified FileIterator<String> does not conform to the VCF specification
    
    java.lang.IllegalArgumentException - if no header line is returned by the specified FileIterator<String>
    
    java.lang.NullPointerException - if it == null
- Method Detail
  - file
```
public java.io.File file()
```
    Returns the file from which data are read, or returns null if the source is standard input.
    
    Returns:
    
    the file from which data are read, or null if the source is standard input
  - nMetaInfoLines
```
public int nMetaInfoLines()
```
    Returns the number of VCF meta-information lines. VCF meta-information lines are lines that precede the VCF header line. A VCF meta-information line must begin with "##".
    
    Returns:
    
    the number of VCF meta-information lines
  - metaInfoLine
```
public VcfMetaInfo metaInfoLine(int index)
```
    Returns the specified VCF meta-information line.
    
    Parameters:
    
    index - a VCF meta-information line index
    
    Returns:
    
    the specified VCF meta-information line
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nMetaInfoLines()
  - headerLine
```
public java.lang.String headerLine()
```
    Returns the VCF header line. The VCF header line begins with "#CHROM".
    
    Returns:
    
    the VCF header line
  - nHeaderFields
```
public int nHeaderFields()
```
    Returns the number of fields in the VCF header line before sample exclusions.
    
    Returns:
    
    the number of fields in the VCF header line before sample exclusions
  - nUnfilteredSamples
```
public int nUnfilteredSamples()
```
    Returns the number of samples before sample exclusions.
    
    Returns:
    
    the number of samples before sample exclusions
  - unfilteredSampleIndex
```
public int unfilteredSampleIndex(int sample)
```
    Returns the index of the specified sample in the the list original list of samples before sample exclusions.
    
    Parameters:
    
    sample - a sample index
    
    Returns:
    
    the index of the specified sample in the the list original list of samples before sample exclusions
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nSamples()
  - nSamples
```
public int nSamples()
```
    Returns the number of samples after sample exclusions.
    
    Returns:
    
    the number of samples after sample exclusions
  - samples
```
public Samples samples()
```
    Return the list of samples after sample exclusions.
    
    Returns:
    
    the list of samples after sample exclusions
  - sampleIds
```
public java.lang.String[] sampleIds()
```
    Returns this.sample().ids().
    
    Returns:
    
    this.sample().ids()
  - toString
```
public java.lang.String toString()
```
    Returns the VCF meta-information lines and the VCF header line used to construct this.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    the VCF meta-information lines and the VCF header line used to construct this

Class VcfHeader

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

HEADER_PREFIX

Constructor Detail

VcfHeader

VcfHeader

Method Detail

file

nMetaInfoLines

metaInfoLine

headerLine

nHeaderFields

nUnfilteredSamples

unfilteredSampleIndex

nSamples

samples

sampleIds

toString