Package htsjdk.samtools.reference

Class ReferenceSequenceFileFactory

java.lang.Object

htsjdk.samtools.reference.ReferenceSequenceFileFactory

public class ReferenceSequenceFileFactory
extends Object

Factory class for creating ReferenceSequenceFile instances for reading reference sequences store in various formats.

Field Summary

Fields

Modifier and Type	Field	Description
static final Set<String>	FASTA_EXTENSIONS	Deprecated. since June 2019 Use FileExtensions.FASTA instead.
static final String	FASTA_INDEX_EXTENSION	Deprecated. since June 2019 Use FileExtensions.FASTA_INDEX instead.

Constructor Summary

Constructors

Constructor	Description
ReferenceSequenceFileFactory()

Method Summary

Modifier and Type	Method	Description
static boolean	canCreateIndexedFastaReader(Path fastaFile)	Checks if the provided FASTA file can be open as indexed.
static File	getDefaultDictionaryForReferenceSequence(File file)	Returns the default dictionary name for a FASTA file.
static Path	getDefaultDictionaryForReferenceSequence(Path path)	Returns the default dictionary name for a FASTA file.
static String	getFastaExtension(Path path)	Returns the FASTA extension for the path.
static Path	getFastaIndexFileName(Path fastaFile)	Returns the index name for a FASTA file.
static ReferenceSequenceFile	getReferenceSequenceFile(File file)	Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
static ReferenceSequenceFile	getReferenceSequenceFile(File file, boolean truncateNamesAtWhitespace)	Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
static ReferenceSequenceFile	getReferenceSequenceFile(File file, boolean truncateNamesAtWhitespace, boolean preferIndexed)	Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
static ReferenceSequenceFile	getReferenceSequenceFile(String source, SeekableStream in, FastaSequenceIndex index)	Return an instance of ReferenceSequenceFile using the given fasta sequence file stream, optional index stream, and no sequence dictionary
static ReferenceSequenceFile	getReferenceSequenceFile(String source, SeekableStream in, FastaSequenceIndex index, SAMSequenceDictionary dictionary, boolean truncateNamesAtWhitespace)	Return an instance of ReferenceSequenceFile using the given fasta sequence file stream and optional index stream and sequence dictionary.
static ReferenceSequenceFile	getReferenceSequenceFile(Path path)	Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
static ReferenceSequenceFile	getReferenceSequenceFile(Path path, boolean truncateNamesAtWhitespace)	Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
static ReferenceSequenceFile	getReferenceSequenceFile(Path path, boolean truncateNamesAtWhitespace, boolean preferIndexed)	Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.
static SAMSequenceDictionary	loadDictionary(InputStream in)	Loads the sequence dictionary from a FASTA file input stream.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

FASTA_EXTENSIONS

@Deprecated
public static final Set<String> FASTA_EXTENSIONS

Deprecated.

since June 2019 Use FileExtensions.FASTA instead.

FASTA_INDEX_EXTENSION

@Deprecated
public static final String FASTA_INDEX_EXTENSION

Deprecated.

since June 2019 Use FileExtensions.FASTA_INDEX instead.

See Also:

• Constant Field Values

Constructor Details

ReferenceSequenceFileFactory

public ReferenceSequenceFileFactory()

Method Details

getReferenceSequenceFile

public static ReferenceSequenceFile getReferenceSequenceFile(File file)

Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it. Sequence names will be truncated at first whitespace, if any.

Parameters:

file - the reference sequence file on disk

getReferenceSequenceFile

public static ReferenceSequenceFile getReferenceSequenceFile(File file,
 boolean truncateNamesAtWhitespace)

Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.

Parameters:

file - the reference sequence file on disk

truncateNamesAtWhitespace - if true, only include the first word of the sequence name

getReferenceSequenceFile

public static ReferenceSequenceFile getReferenceSequenceFile(File file,
 boolean truncateNamesAtWhitespace,
 boolean preferIndexed)

Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.

Parameters:

file - the reference sequence file on disk

truncateNamesAtWhitespace - if true, only include the first word of the sequence name

preferIndexed - if true attempt to return an indexed reader that supports non-linear traversal, else return the non-indexed reader

getReferenceSequenceFile

public static ReferenceSequenceFile getReferenceSequenceFile(Path path)

Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it. Sequence names will be truncated at first whitespace, if any.

Parameters:

path - the reference sequence file on disk

getReferenceSequenceFile

public static ReferenceSequenceFile getReferenceSequenceFile(Path path,
 boolean truncateNamesAtWhitespace)

Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.

Parameters:

path - the reference sequence file on disk

truncateNamesAtWhitespace - if true, only include the first word of the sequence name

getReferenceSequenceFile

public static ReferenceSequenceFile getReferenceSequenceFile(Path path,
 boolean truncateNamesAtWhitespace,
 boolean preferIndexed)

Attempts to determine the type of the reference file and return an instance of ReferenceSequenceFile that is appropriate to read it.

Parameters:

path - the reference sequence file path

truncateNamesAtWhitespace - if true, only include the first word of the sequence name

preferIndexed - if true attempt to return an indexed reader that supports non-linear traversal, else return the non-indexed reader

canCreateIndexedFastaReader

public static boolean canCreateIndexedFastaReader(Path fastaFile)

Checks if the provided FASTA file can be open as indexed.

For a FASTA file to be indexed, it requires to have:

• Associated .fai index (FastaSequenceIndex).
• Associated .gzi index if it is block-compressed (GZIIndex).

Parameters:

fastaFile - the reference sequence file path.

Returns:

true if the file can be open as indexed; false otherwise.

getReferenceSequenceFile

public static ReferenceSequenceFile getReferenceSequenceFile(String source,
 SeekableStream in,
 FastaSequenceIndex index)

Return an instance of ReferenceSequenceFile using the given fasta sequence file stream, optional index stream, and no sequence dictionary

Parameters:

source - The named source of the reference file (used in error messages).

in - The input stream to read the fasta file from.

index - The index, or null to return a non-indexed reader.

getReferenceSequenceFile

public static ReferenceSequenceFile getReferenceSequenceFile(String source,
 SeekableStream in,
 FastaSequenceIndex index,
 SAMSequenceDictionary dictionary,
 boolean truncateNamesAtWhitespace)

Return an instance of ReferenceSequenceFile using the given fasta sequence file stream and optional index stream and sequence dictionary.

Parameters:

source - The named source of the reference file (used in error messages).

in - The input stream to read the fasta file from.

index - The index, or null to return a non-indexed reader.

dictionary - The sequence dictionary, or null if there isn't one.

truncateNamesAtWhitespace - if true, only include the first word of the sequence name

getDefaultDictionaryForReferenceSequence

public static File getDefaultDictionaryForReferenceSequence(File file)

Returns the default dictionary name for a FASTA file.

Parameters:

file - the reference sequence file on disk.

getDefaultDictionaryForReferenceSequence

public static Path getDefaultDictionaryForReferenceSequence(Path path)

Returns the default dictionary name for a FASTA file.

Parameters:

path - the reference sequence file path.

loadDictionary

public static SAMSequenceDictionary loadDictionary(InputStream in)

Loads the sequence dictionary from a FASTA file input stream.

Parameters:

in - the FASTA file input stream.

Returns:

the sequence dictionary, or null if the header has no dictionary or it was empty.

getFastaExtension

public static String getFastaExtension(Path path)

Returns the FASTA extension for the path.

Parameters:

path - the reference sequence file path.

Throws:

IllegalArgumentException - if the file is not a supported reference file.

getFastaIndexFileName

public static Path getFastaIndexFileName(Path fastaFile)

Returns the index name for a FASTA file.

Parameters:

fastaFile - the reference sequence file path.