ReferenceSequenceFileFactory (htsjdk 2.14.3 API)

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 Set<String> FASTA_EXTENSIONS

Fields
Modifier and Type	Field	Description
`static Set<String>`	`FASTA_EXTENSIONS`

Constructor Summary

Constructors
Constructor Description

ReferenceSequenceFileFactory()

Constructors
Constructor	Description
`ReferenceSequenceFileFactory()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`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(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.

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 Set<String> FASTA_EXTENSIONS
```
- Constructor Detail
  - ReferenceSequenceFileFactory
```
public ReferenceSequenceFileFactory()
```
- Method Detail
  - 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
  - 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.
  - 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.

Class ReferenceSequenceFileFactory

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

FASTA_EXTENSIONS

Constructor Detail

ReferenceSequenceFileFactory

Method Detail

getReferenceSequenceFile

getReferenceSequenceFile

getReferenceSequenceFile

getReferenceSequenceFile

getReferenceSequenceFile

getReferenceSequenceFile

getDefaultDictionaryForReferenceSequence

getDefaultDictionaryForReferenceSequence

getFastaExtension

getFastaIndexFileName