VCFFileReader (htsjdk 2.21.3 API)

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

All Implemented Interfaces:

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

Constructor Summary

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`close()`
`static IntervalList`	`fromVcf(java.io.File file)` Deprecated. since July 2018 use `toIntervalList(Path)` instead
`static IntervalList`	`fromVcf(java.io.File file, boolean includeFiltered)` Deprecated. since July 2018 use `toIntervalList(Path, boolean)` instead
`static IntervalList`	`fromVcf(VCFFileReader vcf)` Deprecated. since July 2018 since use `toIntervalList(VCFFileReader)` instead
`static IntervalList`	`fromVcf(VCFFileReader vcf, boolean includeFiltered)` Deprecated. since July 2018 since use `toIntervalList(VCFFileReader, boolean)` instead
`VCFHeader`	`getFileHeader()` Returns the VCFHeader associated with this VCF/BCF file.
`static SAMSequenceDictionary`	`getSequenceDictionary(java.io.File file)` Returns the SAMSequenceDictionary from the provided VCF file.
`static SAMSequenceDictionary`	`getSequenceDictionary(java.nio.file.Path path)` Returns the SAMSequenceDictionary from the provided VCF file.
`static boolean`	`isBCF(java.io.File file)` Returns true if the given file appears to be a BCF file.
`static boolean`	`isBCF(java.nio.file.Path path)` Returns true if the given path appears to be a BCF file.
`boolean`	`isQueryable()` A method to check if the reader is query-able, i.e.
`CloseableIterator<VariantContext>`	`iterator()` Returns an iterator over all records in this VCF/BCF file.
`CloseableIterator<VariantContext>`	`query(Locatable locatable)` Queries for records overlapping the `Locatable` specified.
`CloseableIterator<VariantContext>`	`query(java.lang.String chrom, int start, int end)` Queries for records overlapping the region specified.
`IntervalList`	`toIntervalList()` Converts the underlying VCFFileReader to an IntervalList.
`IntervalList`	`toIntervalList(boolean includeFiltered)`
`static IntervalList`	`toIntervalList(java.nio.file.Path path)` 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`	`toIntervalList(java.nio.file.Path path, boolean includeFiltered)`
`static IntervalList`	`toIntervalList(VCFFileReader vcf)` Converts a vcf to an IntervalList.
`static IntervalList`	`toIntervalList(VCFFileReader vcf, boolean includeFiltered)` Converts a `VCFFileReader` to an IntervalList.
`static java.util.Iterator<Interval>`	`toIntervals(VCFFileReader vcf, boolean includeFiltered)` Converts a `VCFFileReader` to an `Iterator` The name field of the Interval is taken from the ID field of the variant, if it exists.

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(java.io.File file)
```
    Constructs a VCFFileReader that requires the index to be present.
  - VCFFileReader
```
public VCFFileReader(java.io.File file,
                     java.io.File indexFile)
```
    Constructs a VCFFileReader with a specified index.
  - VCFFileReader
```
public VCFFileReader(java.io.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(java.io.File file,
                     java.io.File indexFile,
                     boolean requireIndex)
```
    Allows construction of a VCFFileReader with a specified index file.
  - VCFFileReader
```
public VCFFileReader(java.nio.file.Path path)
```
    Constructs a VCFFileReader that requires the index to be present.
  - VCFFileReader
```
public VCFFileReader(java.nio.file.Path path,
                     java.nio.file.Path indexPath)
```
    Constructs a VCFFileReader with a specified index.
  - VCFFileReader
```
public VCFFileReader(java.nio.file.Path path,
                     boolean requireIndex)
```
    Allows construction of a VCFFileReader that will or will not assert the presence of an index as desired.
  - VCFFileReader
```
public VCFFileReader(java.nio.file.Path path,
                     java.nio.file.Path indexPath,
                     boolean requireIndex)
```
    Allows construction of a VCFFileReader with a specified index path.
- Method Detail
  - isBCF
```
public static boolean isBCF(java.io.File file)
```
    Returns true if the given file appears to be a BCF file.
  - isBCF
```
public static boolean isBCF(java.nio.file.Path path)
```
    Returns true if the given path appears to be a BCF file.
  - getSequenceDictionary
```
public static SAMSequenceDictionary getSequenceDictionary(java.io.File file)
```
    Returns the SAMSequenceDictionary from the provided VCF file.
  - getSequenceDictionary
```
public static SAMSequenceDictionary getSequenceDictionary(java.nio.file.Path path)
```
    Returns the SAMSequenceDictionary from the provided VCF file.
  - toIntervalList
```
public static IntervalList toIntervalList(java.nio.file.Path path)
```
    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:
    
    path - a VCF
    
    Returns:
  - toIntervalList
```
public static IntervalList toIntervalList(java.nio.file.Path path,
                                          boolean includeFiltered)
```
  - fromVcf
```
@Deprecated
public static IntervalList fromVcf(java.io.File file)
```
    Deprecated. since July 2018 use toIntervalList(Path) instead
    
    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 - a VCF
    
    Returns:
    
    an IntervalList
  - fromVcf
```
@Deprecated
public static IntervalList fromVcf(java.io.File file,
                                               boolean includeFiltered)
```
    Deprecated. since July 2018 use toIntervalList(Path, boolean) instead
    
    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:
  - toIntervalList
```
public IntervalList toIntervalList()
```
    Converts the underlying VCFFileReader 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 on un-named intervals. Will use the "END" tag in the INFO field as the end of the interval (if exists).
    
    Returns:
    
    an IntervalList constructed from input vcf
  - toIntervalList
```
public IntervalList toIntervalList(boolean includeFiltered)
```
  - fromVcf
```
@Deprecated
public static IntervalList fromVcf(VCFFileReader vcf)
```
    Deprecated. since July 2018 since use toIntervalList(VCFFileReader) instead
    
    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
  - toIntervalList
```
public static IntervalList toIntervalList(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
```
@Deprecated
public static IntervalList fromVcf(VCFFileReader vcf,
                                               boolean includeFiltered)
```
    Deprecated. since July 2018 since use toIntervalList(VCFFileReader, boolean) instead
    
    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
  - toIntervalList
```
public static IntervalList toIntervalList(VCFFileReader vcf,
                                          boolean includeFiltered)
```
    Converts a VCFFileReader to an IntervalList. The name field of the Interval 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
  - toIntervals
```
public static java.util.Iterator<Interval> toIntervals(VCFFileReader vcf,
                                                       boolean includeFiltered)
```
    Converts a VCFFileReader to an Iterator The name field of the Interval 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:
    
    a Iterator constructed from input vcf
  - 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 java.lang.Iterable<VariantContext>
  - query
```
public CloseableIterator<VariantContext> query(java.lang.String chrom,
                                               int start,
                                               int end)
```
    Queries for records overlapping the region specified. Note that this method requires VCF files with an associated index. If no index exists a TribbleException will be thrown.
    
    Parameters:
    
    chrom - the chomosome to query
    
    start - query interval start
    
    end - query interval end
    
    Returns:
    
    non-null iterator over VariantContexts
  - query
```
public CloseableIterator<VariantContext> query(Locatable locatable)
```
    Queries for records overlapping the Locatable specified. Note that this method requires VCF files with an associated index. If no index exists a TribbleException will be thrown.
    
    Returns:
    
    non-null iterator over VariantContexts
  - close
```
public void close()
```
    Specified by:
    
    close in interface java.io.Closeable
    
    Specified by:
    
    close in interface java.lang.AutoCloseable
  - isQueryable
```
public boolean isQueryable()
```
    A method to check if the reader is query-able, i.e. if a call to query(String, int, int) can be successful
    
    Returns:
    
    true if the reader can be queried, i.e. if the underlying Tribble reader is queryable.

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

VCFFileReader

VCFFileReader

VCFFileReader

VCFFileReader

Method Detail

isBCF

isBCF

getSequenceDictionary

getSequenceDictionary

toIntervalList

toIntervalList

fromVcf

fromVcf

toIntervalList

toIntervalList

fromVcf

toIntervalList

fromVcf

toIntervalList

toIntervals

getFileHeader

iterator

query

query

close

isQueryable