VCFFileReader (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.variant.vcf.VCFFileReader

All Implemented Interfaces:

Closeable, AutoCloseable, Iterable<VariantContext>
```
public class VCFFileReader
extends Object
implements Closeable, Iterable<VariantContext>
```
Simplified interface for reading from VCF/BCF files.

Constructor Summary

Constructors
Constructor and Description
`VCFFileReader(File file)` Constructs a VCFFileReader that requires the index to be present.
`VCFFileReader(File file, boolean requireIndex)` Allows construction of a VCFFileReader that will or will not assert the presence of an index as desired.
`VCFFileReader(File file, File indexFile)` Constructs a VCFFileReader with a specified index.
`VCFFileReader(File file, File indexFile, boolean requireIndex)` Allows construction of a VCFFileReader with a specified index file.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close()`
`static IntervalList`	`fromVcf(File file)` Parse a VCF file and convert to an IntervalList The name field of the IntervalList is taken from the ID field of the variant, if it exists.
`static IntervalList`	`fromVcf(File file, boolean includeFiltered)`
`static IntervalList`	`fromVcf(VCFFileReader vcf)` Converts a vcf to an IntervalList.
`static IntervalList`	`fromVcf(VCFFileReader vcf, boolean includeFiltered)`
`VCFHeader`	`getFileHeader()` Returns the VCFHeader associated with this VCF/BCF file.
`static SAMSequenceDictionary`	`getSequenceDictionary(File file)` Returns the SAMSequenceDictionary from the provided VCF file.
`static boolean`	`isBCF(File file)` Returns true if the given file appears to be a BCF file.
`CloseableIterator<VariantContext>`	`iterator()` Returns an iterator over all records in this VCF/BCF file.
`CloseableIterator<VariantContext>`	`query(String chrom, int start, int end)` Queries for records within the region specified.

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

Methods inherited from interface java.lang.Iterable
forEach, spliterator

- Constructor Detail
  - VCFFileReader
```
public VCFFileReader(File file)
```
    Constructs a VCFFileReader that requires the index to be present.
  - VCFFileReader
```
public VCFFileReader(File file,
                     File indexFile)
```
    Constructs a VCFFileReader with a specified index.
  - VCFFileReader
```
public VCFFileReader(File file,
                     boolean requireIndex)
```
    Allows construction of a VCFFileReader that will or will not assert the presence of an index as desired.
  - VCFFileReader
```
public VCFFileReader(File file,
                     File indexFile,
                     boolean requireIndex)
```
    Allows construction of a VCFFileReader with a specified index file.
- Method Detail
  - isBCF
```
public static boolean isBCF(File file)
```
    Returns true if the given file appears to be a BCF file.
  - getSequenceDictionary
```
public static SAMSequenceDictionary getSequenceDictionary(File file)
```
    Returns the SAMSequenceDictionary from the provided VCF file.
  - fromVcf
```
public static IntervalList fromVcf(File file)
```
    Parse a VCF file and convert to an IntervalList The name field of the IntervalList is taken from the ID field of the variant, if it exists. if not, creates a name of the format interval-n where n is a running number that increments only on un-named intervals
    
    Parameters:
    
    file -
    
    Returns:
  - fromVcf
```
public static IntervalList fromVcf(File file,
                                   boolean includeFiltered)
```
  - fromVcf
```
public static IntervalList fromVcf(VCFFileReader vcf)
```
    Converts a vcf to an IntervalList. The name field of the IntervalList is taken from the ID field of the variant, if it exists. If not, creates a name of the format interval-n where n is a running number that increments only on un-named intervals Will use a "END" tag in the info field as the end of the interval (if exists).
    
    Parameters:
    
    vcf - the vcfReader to be used for the conversion
    
    Returns:
    
    an IntervalList constructed from input vcf
  - fromVcf
```
public static IntervalList fromVcf(VCFFileReader vcf,
                                   boolean includeFiltered)
```
  - getFileHeader
```
public VCFHeader getFileHeader()
```
    Returns the VCFHeader associated with this VCF/BCF file.
  - iterator
```
public CloseableIterator<VariantContext> iterator()
```
    Returns an iterator over all records in this VCF/BCF file.
    
    Specified by:
    
    iterator in interface Iterable<VariantContext>
  - query
```
public CloseableIterator<VariantContext> query(String chrom,
                                               int start,
                                               int end)
```
    Queries for records within the region specified.
  - close
```
public void close()
```
    Specified by:
    
    close in interface Closeable
    
    Specified by:
    
    close in interface AutoCloseable

Class VCFFileReader

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Detail

VCFFileReader

VCFFileReader

VCFFileReader

VCFFileReader

Method Detail

isBCF

getSequenceDictionary

fromVcf

fromVcf

fromVcf

fromVcf

getFileHeader

iterator

query

close