public class ReferenceSequenceFileFactory extends Object
Modifier and Type | Field | Description |
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static Set<String> |
FASTA_EXTENSIONS |
Constructor | Description |
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ReferenceSequenceFileFactory() |
Modifier and Type | Method | Description |
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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.
|
public static ReferenceSequenceFile getReferenceSequenceFile(File file)
file
- the reference sequence file on diskpublic static ReferenceSequenceFile getReferenceSequenceFile(File file, boolean truncateNamesAtWhitespace)
file
- the reference sequence file on disktruncateNamesAtWhitespace
- if true, only include the first word of the sequence namepublic static ReferenceSequenceFile getReferenceSequenceFile(File file, boolean truncateNamesAtWhitespace, boolean preferIndexed)
file
- the reference sequence file on disktruncateNamesAtWhitespace
- if true, only include the first word of the sequence namepreferIndexed
- if true attempt to return an indexed reader that supports non-linear traversal, else return the non-indexed readerpublic static ReferenceSequenceFile getReferenceSequenceFile(Path path)
path
- the reference sequence file on diskpublic static ReferenceSequenceFile getReferenceSequenceFile(Path path, boolean truncateNamesAtWhitespace)
path
- the reference sequence file on disktruncateNamesAtWhitespace
- if true, only include the first word of the sequence namepublic static ReferenceSequenceFile getReferenceSequenceFile(Path path, boolean truncateNamesAtWhitespace, boolean preferIndexed)
path
- the reference sequence file pathtruncateNamesAtWhitespace
- if true, only include the first word of the sequence namepreferIndexed
- if true attempt to return an indexed reader that supports non-linear traversal, else return the non-indexed readerpublic static File getDefaultDictionaryForReferenceSequence(File file)
file
- the reference sequence file on disk.public static Path getDefaultDictionaryForReferenceSequence(Path path)
path
- the reference sequence file path.public static String getFastaExtension(Path path)
path
- the reference sequence file path.IllegalArgumentException
- if the file is not a supported reference file.