htsjdk.samtools.reference

Class ReferenceSequenceFileFactory

java.lang.Object

htsjdk.samtools.reference.ReferenceSequenceFileFactory

public class ReferenceSequenceFileFactory
extends java.lang.Object

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

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.Set<java.lang.String>	FASTA_EXTENSIONS

Constructor Summary

Constructors

Constructor and Description
ReferenceSequenceFileFactory()

Method Summary

Modifier and Type	Method and Description
static java.io.File	getDefaultDictionaryForReferenceSequence(java.io.File file) Returns the default dictionary name for a FASTA file.
static java.nio.file.Path	getDefaultDictionaryForReferenceSequence(java.nio.file.Path path) Returns the default dictionary name for a FASTA file.
static java.lang.String	getFastaExtension(java.nio.file.Path path) Returns the FASTA extension for the path.
static java.nio.file.Path	getFastaIndexFileName(java.nio.file.Path fastaFile) Returns the index name for a FASTA file.
static ReferenceSequenceFile	getReferenceSequenceFile(java.io.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(java.io.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(java.io.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(java.nio.file.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(java.nio.file.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(java.nio.file.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.

Methods inherited from class java.lang.Object

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

Field Detail

FASTA_EXTENSIONS

public static final java.util.Set<java.lang.String> FASTA_EXTENSIONS

Constructor Detail

ReferenceSequenceFileFactory

public ReferenceSequenceFileFactory()

Method Detail

getReferenceSequenceFile

public static ReferenceSequenceFile getReferenceSequenceFile(java.io.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(java.io.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(java.io.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(java.nio.file.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(java.nio.file.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(java.nio.file.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

getDefaultDictionaryForReferenceSequence

public static java.io.File getDefaultDictionaryForReferenceSequence(java.io.File file)

Returns the default dictionary name for a FASTA file.

Parameters:

file - the reference sequence file on disk.

getDefaultDictionaryForReferenceSequence

public static java.nio.file.Path getDefaultDictionaryForReferenceSequence(java.nio.file.Path path)

Returns the default dictionary name for a FASTA file.

Parameters:

path - the reference sequence file path.

getFastaExtension

public static java.lang.String getFastaExtension(java.nio.file.Path path)

Returns the FASTA extension for the path.

Parameters:

path - the reference sequence file path.

Throws:

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

getFastaIndexFileName

public static java.nio.file.Path getFastaIndexFileName(java.nio.file.Path fastaFile)

Returns the index name for a FASTA file.

Parameters:

fastaFile - the reference sequence file path.