VCFIndex

gngs.VCFIndex

```
@groovy.transform.CompileStatic
class VCFIndex
extends java.lang.Object
```
Support for querying indexed VCF files via random access.
In general, if you only want to access a small region of a VCF (eg: to look up variants in a specific region, etc) then this class is your best bet. If, alternatively, you have a smaller VCF file (say, less than 100,000 lines) and you expect to query a significant number of the variants in it, you should go straight for the gngs.VCF class instead and just load everything into memory.
The VCFIndex class is highly optimised for random access to VCF contents. It uses memory mapped files to buffer the VCF to memory to minimize the actual hits to the file system.
Using the VCFIndex class to look up variants in a region is very simple:
```
 VCFIndex index = new VCFIndex("test.vcf")
 index.query("chrX",1000,2000) { Variant v ->
  println "Variant $v is in the range chrX:1000-2000"
 }
 
```
You can also easily test if a Variant exists within the VCF file:
```
 Variant v = new Variant(chr:"chrX", alt:"A", ref:"T")
 VCFIndex index = new VCFIndex("test.vcf")
 if(v in index)
      println "Variant $v is found in test.vcf"
 
```
Authors:
simon.sadedin@mcri.edu.au

Nested Class Summary

Nested classes
Modifiers	Name	Description
`class`	`VCFIndex.1`

Field Summary

Fields
Modifiers	Name	Description
`static int`	`BUFFER_SIZE`	A 256 kb memory buffer that will try to minimize operations on the indexed file
`static int`	`ONE_GIG`

Properties Summary

Properties
Type	Name and description
`java.lang.String`	`fileName` File name of VCF file
`gngs.VCF`	`headerVCF` A dummy VCF used to parse / hold the header information
`htsjdk.tribble.index.Index`	`index` Indexes used for random access to large VCFs.
`java.io.RandomAccessFile`	`indexedFile` Raw file corresponding to the VCF
`java.util.List<MappedByteBuffer>`	`vcfBuffers`

Constructor Summary

Constructors
Constructor and description
`VCFIndex ()`
`VCFIndex (java.lang.String fileName)` Load and index for the given VCF file

Methods Summary

Methods
Type Params	Return Type	Name and description
	`gngs.Variant`	`contains(gngs.Variant v)` Returns true if this VCF contains the specified variant
	`gngs.Variant`	`find(java.lang.String chr, int start, int end, groovy.lang.Closure c)` Find the first variant in an interval that returns true from the given closure
	`java.util.Map`	`findAnnovarVariant(java.lang.String chr, java.lang.Object start, java.lang.Object end, java.lang.String obs, int windowSize)` Attempts to locate the given Annovar variant in this VCF file.
	`boolean`	`isCase(gngs.Variant v)`
	`java.util.Iterator<gngs.Variant>`	`iterator(java.lang.String chr, int start, int end)`
	`void`	`query(IRegion r, groovy.lang.Closure c)`
	`void`	`query(java.lang.String chr, int start, int end, groovy.lang.Closure c)`
	`void`	`queryIdx(java.lang.String chr, int start, int end, groovy.lang.Closure c)` Query the current VCF file for all variants in the specified region
	`void`	`queryTabix(java.lang.String chr, int start, int end, groovy.lang.Closure c)`

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class java.lang.Object`	`java.lang.Object#wait(long), java.lang.Object#wait(long, int), 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()`

- Field Detail
  - public static final int BUFFER_SIZE
    
    A 256 kb memory buffer that will try to minimize operations on the indexed file
  - public static final int ONE_GIG
- Property Detail
  - java.lang.String fileName
    
    File name of VCF file
  - gngs.VCF headerVCF
    
    A dummy VCF used to parse / hold the header information
  - htsjdk.tribble.index.Index index
    
    Indexes used for random access to large VCFs. Used with *.query() functions
  - java.io.RandomAccessFile indexedFile
    
    Raw file corresponding to the VCF
  - java.util.List<MappedByteBuffer> vcfBuffers
- Constructor Detail
  - VCFIndex()
  - VCFIndex(java.lang.String fileName)
    
    Load and index for the given VCF file
    Parameters:
    fileName
- Method Detail
  - gngs.Variant contains(gngs.Variant v)
    
    Returns true if this VCF contains the specified variant
    IMPORTANT: the other variant is required to contain only a single allele for this function to return correct results!
    Parameters:
    v - Variant to test for
    Returns:
    The variant iff this VCF contains the variant, null otherwise
  - gngs.Variant find(java.lang.String chr, int start, int end, groovy.lang.Closure c)
    
    Find the first variant in an interval that returns true from the given closure
    Example:
```
 VCFIndex index = new VCFIndex("test.vcf")
 Variant v = index.find("chrX", 1000,2000) { it.type == "DEL" && it.size() > 4 }
 println "First deletion greater than 4 bases in size is $v"
 
```
    Parameters:
    chr - Chromosome to scan
    start - Starting position in chromosome
    end - End position in chromosome
    c - Closure to call, passing each Variant from the VCF as the first argument.
    Returns:
    The first Variant in the specified range for which the Closure c returns an argument that does not evaluate to false (null, 0, etc.)
  - @groovy.transform.CompileDynamic java.util.Map findAnnovarVariant(java.lang.String chr, java.lang.Object start, java.lang.Object end, java.lang.String obs, int windowSize)
    
    Attempts to locate the given Annovar variant in this VCF file.
    Annovar is a popular annotation tool which outputs results in its own proprietary CSV format. Unfortunately, this format does not use the same reference coordinates, and thus an Annovar variant is not directly translatable to a VCF variant, and it is necessary to scan a range of indexes in an original VCF file to locate the corresponding Annovar variant. This function implements the required logic.
    Parameters:
    chr - chromosome / reference sequence
    start - Annovar variant start position
    end - Annovar variant end position
    windowSize - the size of window to scan. VCF files can include overlapping variants in arbitrarily long windows. Thus it is necessary to start scanning the VCF significantly before the location of the actual start of the DNA change to be sure of finding the Annovar variant. In general, the window size should be as large as the largest indels you expect to have in your VCF file.
    Returns:
    if the variant is found, a map containing "variant" and "allele" entries. the variant is the Variant object, while the allele is the zero-based index of the allele within the Variant that corresponds to the Annovar variant specified.
  - boolean isCase(gngs.Variant v)
  - @groovy.transform.CompileStatic java.util.Iterator<gngs.Variant> iterator(java.lang.String chr, int start, int end)
  - void query(IRegion r, groovy.lang.Closure c)
  - void query(java.lang.String chr, int start, int end, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [gngs.Variant]) groovy.lang.Closure c)
  - @groovy.transform.CompileStatic void queryIdx(java.lang.String chr, int start, int end, groovy.lang.Closure c)
    
    Query the current VCF file for all variants in the specified region
    Parameters:
    chr - Chromosome / Sequence name
    start - Start position
    end - End position
    c - Closure to call back
  - void queryTabix(java.lang.String chr, int start, int end, groovy.lang.Closure c)

Groovy Documentation

[Groovy] Class VCFIndex

Nested Class Summary

Field Summary

Properties Summary

Constructor Summary

Methods Summary

Inherited Methods Summary

Field Detail

public static final int BUFFER_SIZE

public static final int ONE_GIG

Property Detail

java.lang.String fileName

gngs.VCF headerVCF

htsjdk.tribble.index.Index index

java.io.RandomAccessFile indexedFile

java.util.List<MappedByteBuffer> vcfBuffers

Constructor Detail

VCFIndex()

VCFIndex(java.lang.String fileName)

Method Detail

gngs.Variant contains(gngs.Variant v)

gngs.Variant find(java.lang.String chr, int start, int end, groovy.lang.Closure c)

@groovy.transform.CompileDynamic java.util.Map findAnnovarVariant(java.lang.String chr, java.lang.Object start, java.lang.Object end, java.lang.String obs, int windowSize)

boolean isCase(gngs.Variant v)

@groovy.transform.CompileStatic java.util.Iterator<gngs.Variant> iterator(java.lang.String chr, int start, int end)

void query(IRegion r, groovy.lang.Closure c)

void query(java.lang.String chr, int start, int end, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [gngs.Variant]) groovy.lang.Closure c)

@groovy.transform.CompileStatic void queryIdx(java.lang.String chr, int start, int end, groovy.lang.Closure c)

void queryTabix(java.lang.String chr, int start, int end, groovy.lang.Closure c)