public class ReferenceSequenceFileFactory
extends java.lang.Object
Modifier and Type | Field and Description |
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static java.util.Set<java.lang.String> |
FASTA_EXTENSIONS |
Constructor and Description |
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ReferenceSequenceFileFactory() |
Modifier and Type | Method and Description |
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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.
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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.
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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.
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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.
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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.
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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.
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public static ReferenceSequenceFile getReferenceSequenceFile(java.io.File file)
file
- the reference sequence file on diskpublic static ReferenceSequenceFile getReferenceSequenceFile(java.io.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(java.io.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(java.nio.file.Path path)
path
- the reference sequence file on diskpublic static ReferenceSequenceFile getReferenceSequenceFile(java.nio.file.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(java.nio.file.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 reader