Package htsjdk.samtools.reference

Class FastaSequenceFile

java.lang.Object

htsjdk.samtools.reference.FastaSequenceFile

All Implemented Interfaces:

ReferenceSequenceFile, Closeable, AutoCloseable

public class FastaSequenceFile
extends Object

Implementation of ReferenceSequenceFile for reading from FASTA files.

Constructor Summary

Constructors

Constructor	Description
FastaSequenceFile(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 Type	Method	Description
void	close()	It's good to call this to free up memory.
protected SAMSequenceDictionary	findAndLoadSequenceDictionary(Path fasta)	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	getAbsolutePath()	Returns the full path to the reference file.
protected Path	getPath()	Returns the path to the reference file.
ReferenceSequence	getSequence(String contig)	default implementation -- override if index is supported
SAMSequenceDictionary	getSequenceDictionary()	Returns the list of sequence records associated with the reference sequence if found otherwise null.
protected String	getSource()	Returns the named source of the reference file.
ReferenceSequence	getSubsequenceAt(String contig, long start, long stop)	default implementation -- override if index is supported
boolean	isIndexed()	default implementation -- override if index is supported
ReferenceSequence	nextSequence()	Retrieves 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.
String	toString()	Returns the full path to the reference file, or the source if no path was specified.

Methods inherited from class java.lang.Object

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

Constructor Details

FastaSequenceFile

public FastaSequenceFile(File file,
 boolean truncateNamesAtWhitespace)

Constructs a FastaSequenceFile that reads from the specified file.

FastaSequenceFile

public FastaSequenceFile(Path path,
 boolean truncateNamesAtWhitespace)

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).

Method Details

close

public void close()

It's good to call this to free up memory.

nextSequence

public ReferenceSequence 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

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

protected SAMSequenceDictionary findAndLoadSequenceDictionary(Path fasta)

Attempts to find and load the sequence dictionary if present.

findSequenceDictionary

@Deprecated
protected static File findSequenceDictionary(File file)

Deprecated.

use findSequenceDictionary(Path) instead.

findSequenceDictionary

protected static Path findSequenceDictionary(Path fastaPath)

Attempts to locate the sequence dictionary file adjacent to the reference fasta file.

getPath

protected Path getPath()

Returns the path to the reference file.

getSource

protected String getSource()

Returns the named source of the reference file.

getSequenceDictionary

public SAMSequenceDictionary getSequenceDictionary()

Returns the list of sequence records associated with the reference sequence if found otherwise null.

Specified by:

getSequenceDictionary in interface ReferenceSequenceFile

Returns:

a list of sequence records representing the sequences in this reference file

getAbsolutePath

protected String getAbsolutePath()

Returns the full path to the reference file.

toString

public String toString()

Returns the full path to the reference file, or the source if no path was specified.

Specified by:

toString in interface ReferenceSequenceFile

Overrides:

toString in class Object

Returns:

Reference name, file name, or something other human-readable representation.

isIndexed

public boolean isIndexed()

default implementation -- override if index is supported

Specified by:

isIndexed in interface ReferenceSequenceFile

Returns:

true if getSequence and getSubsequenceAt methods are allowed.

getSequence

public ReferenceSequence getSequence(String contig)

default implementation -- override if index is supported

Specified by:

getSequence in interface ReferenceSequenceFile

Parameters:

contig - contig whose data should be returned.

Returns:

The full sequence associated with this contig.

getSubsequenceAt

public ReferenceSequence getSubsequenceAt(String contig,
 long start,
 long stop)

default implementation -- override if index is supported

Specified by:

getSubsequenceAt in interface ReferenceSequenceFile

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.