Package htsjdk.samtools.reference
Class FastaSequenceFile
java.lang.Object
htsjdk.samtools.reference.FastaSequenceFile
- All Implemented Interfaces:
ReferenceSequenceFile
,Closeable
,AutoCloseable
Implementation of ReferenceSequenceFile for reading from FASTA files.
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Constructor Summary
ConstructorDescriptionFastaSequenceFile
(File file, boolean truncateNamesAtWhitespace) Constructs a FastaSequenceFile that reads from the specified file.FastaSequenceFile
(String source, SeekableStream seekableStream, SAMSequenceDictionary dictionary, boolean truncateNamesAtWhitespace) Constructs a FastaSequenceFile that reads from the specified stream (which must not be compressed, i.e.FastaSequenceFile
(Path path, boolean truncateNamesAtWhitespace) Constructs a FastaSequenceFile that reads from the specified file. -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
It's good to call this to free up memory.protected SAMSequenceDictionary
Attempts to find and load the sequence dictionary if present.protected static File
findSequenceDictionary
(File file) Deprecated.use findSequenceDictionary(Path) instead.protected static Path
findSequenceDictionary
(Path fastaPath) Attempts to locate the sequence dictionary file adjacent to the reference fasta file.protected String
Returns the full path to the reference file.protected Path
getPath()
Returns the path to the reference file.getSequence
(String contig) default implementation -- override if index is supportedReturns the list of sequence records associated with the reference sequence if found otherwise null.protected String
Returns the named source of the reference file.getSubsequenceAt
(String contig, long start, long stop) default implementation -- override if index is supportedboolean
default implementation -- override if index is supportedRetrieves the next whole sequences from the file.void
reset()
Resets the ReferenceSequenceFile so that the next call to nextSequence() will return the first sequence in the file.toString()
Returns the full path to the reference file, or the source if no path was specified.
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Constructor Details
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FastaSequenceFile
Constructs a FastaSequenceFile that reads from the specified file. -
FastaSequenceFile
Constructs a FastaSequenceFile that reads from the specified file. -
FastaSequenceFile
public FastaSequenceFile(String source, SeekableStream seekableStream, SAMSequenceDictionary dictionary, boolean truncateNamesAtWhitespace) Constructs a FastaSequenceFile that reads from the specified stream (which must not be compressed, i.e. the caller is responsible for decompressing the stream).
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Method Details
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close
public void close()It's good to call this to free up memory. -
nextSequence
Description copied from interface:ReferenceSequenceFile
Retrieves the next whole sequences from the file.- Returns:
- a ReferenceSequence or null if at the end of the file
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reset
public void reset()Description copied from interface:ReferenceSequenceFile
Resets the ReferenceSequenceFile so that the next call to nextSequence() will return the first sequence in the file. -
findAndLoadSequenceDictionary
Attempts to find and load the sequence dictionary if present. -
findSequenceDictionary
Deprecated.use findSequenceDictionary(Path) instead. -
findSequenceDictionary
Attempts to locate the sequence dictionary file adjacent to the reference fasta file. -
getPath
Returns the path to the reference file. -
getSource
Returns the named source of the reference file. -
getSequenceDictionary
Returns the list of sequence records associated with the reference sequence if found otherwise null.- Specified by:
getSequenceDictionary
in interfaceReferenceSequenceFile
- Returns:
- a list of sequence records representing the sequences in this reference file
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getAbsolutePath
Returns the full path to the reference file. -
toString
Returns the full path to the reference file, or the source if no path was specified.- Specified by:
toString
in interfaceReferenceSequenceFile
- Overrides:
toString
in classObject
- Returns:
- Reference name, file name, or something other human-readable representation.
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isIndexed
public boolean isIndexed()default implementation -- override if index is supported- Specified by:
isIndexed
in interfaceReferenceSequenceFile
- Returns:
- true if getSequence and getSubsequenceAt methods are allowed.
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getSequence
default implementation -- override if index is supported- Specified by:
getSequence
in interfaceReferenceSequenceFile
- Parameters:
contig
- contig whose data should be returned.- Returns:
- The full sequence associated with this contig.
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getSubsequenceAt
default implementation -- override if index is supported- Specified by:
getSubsequenceAt
in interfaceReferenceSequenceFile
- Parameters:
contig
- Contig whose subsequence to retrieve.start
- inclusive, 1-based start of region.stop
- inclusive, 1-based stop of region.- Returns:
- The partial reference sequence associated with this range.
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