Package htsjdk.variant.vcf

Class VCFFileReader

java.lang.Object

htsjdk.variant.vcf.VCFFileReader

All Implemented Interfaces:

VCFReader, Closeable, AutoCloseable, Iterable<VariantContext>

public class VCFFileReader
extends Object
implements VCFReader

Simplified interface for reading from VCF/BCF files.

Constructor Summary

Constructors

Constructor	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.
VCFFileReader(Path path)	Constructs a VCFFileReader that requires the index to be present.
VCFFileReader(Path path, boolean requireIndex)	Allows construction of a VCFFileReader that will or will not assert the presence of an index as desired.
VCFFileReader(Path path, Path indexPath)	Constructs a VCFFileReader with a specified index.
VCFFileReader(Path path, Path indexPath, boolean requireIndex)	Allows construction of a VCFFileReader with a specified index path.

Method Summary

Modifier and Type	Method	Description
void	close()
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
static IntervalList	fromVcf(File file)	Deprecated. since July 2018 use toIntervalList(Path) instead
static IntervalList	fromVcf(File file, boolean includeFiltered)	Deprecated. since July 2018 use toIntervalList(Path, boolean) instead
final VCFHeader	getFileHeader()	Synonym of getHeader()
VCFHeader	getHeader()	Returns the VCFHeader associated with this VCF/BCF file.
static SAMSequenceDictionary	getSequenceDictionary(File file)	Returns the SAMSequenceDictionary from the provided VCF file.
static SAMSequenceDictionary	getSequenceDictionary(Path path)	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.
static boolean	isBCF(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(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(VCFFileReader vcf)	Converts a vcf to an IntervalList.
static IntervalList	toIntervalList(VCFFileReader vcf, boolean includeFiltered)	Converts a VCFFileReader to an IntervalList.
static IntervalList	toIntervalList(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(Path path, boolean includeFiltered)
static Iterator<Interval>	toIntervals(VCFFileReader vcf, boolean includeFiltered)	Converts a VCFFileReader to an Iterator<Interval> 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

Methods inherited from interface htsjdk.variant.vcf.VCFReader

query

Constructor Details

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.

VCFFileReader

public VCFFileReader(Path path)

Constructs a VCFFileReader that requires the index to be present.

VCFFileReader

public VCFFileReader(Path path,
 Path indexPath)

Constructs a VCFFileReader with a specified index.

VCFFileReader

public VCFFileReader(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(Path path,
 Path indexPath,
 boolean requireIndex)

Allows construction of a VCFFileReader with a specified index path.

Method Details

isBCF

public static boolean isBCF(File file)

Returns true if the given file appears to be a BCF file.

isBCF

public static boolean isBCF(Path path)

Returns true if the given path appears to be a BCF file.

getSequenceDictionary

public static SAMSequenceDictionary getSequenceDictionary(File file)

Returns the SAMSequenceDictionary from the provided VCF file.

getSequenceDictionary

public static SAMSequenceDictionary getSequenceDictionary(Path path)

Returns the SAMSequenceDictionary from the provided VCF file.

toIntervalList

public static IntervalList toIntervalList(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(Path path,
 boolean includeFiltered)

fromVcf

@Deprecated
public static IntervalList fromVcf(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(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 Iterator<Interval> toIntervals(VCFFileReader vcf,
 boolean includeFiltered)

Converts a VCFFileReader to an Iterator<Interval> 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

getHeader

public VCFHeader getHeader()

Returns the VCFHeader associated with this VCF/BCF file.

Specified by:

getHeader in interface VCFReader

getFileHeader

public final VCFHeader getFileHeader()

Synonym of getHeader()

iterator

public CloseableIterator<VariantContext> iterator()

Returns an iterator over all records in this VCF/BCF file.

Specified by:

iterator in interface Iterable<VariantContext>

Specified by:

iterator in interface VCFReader

query

public CloseableIterator<VariantContext> query(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.

Specified by:

query in interface VCFReader

Parameters:

chrom - the chomosome to query

start - query interval start

end - query interval end

Returns:

non-null iterator over VariantContexts

close

public void close()

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

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

Specified by:

isQueryable in interface VCFReader

Returns:

true if the reader can be queried, i.e. if the underlying Tribble reader is queryable.