htsjdk.samtools.reference

Class IndexedFastaSequenceFile

java.lang.Object

htsjdk.samtools.reference.IndexedFastaSequenceFile

All Implemented Interfaces:

ReferenceSequenceFile, java.io.Closeable, java.lang.AutoCloseable

public class IndexedFastaSequenceFile
extends java.lang.Object
implements java.io.Closeable

A fasta file driven by an index for fast, concurrent lookups. Supports two interfaces: the ReferenceSequenceFile for old-style, stateful lookups and a direct getter.

Field Summary

Fields

Modifier and Type	Field and Description
protected SAMSequenceDictionary	sequenceDictionary

Constructor Summary

Constructors

Constructor and Description
IndexedFastaSequenceFile(java.io.File file) Open the given indexed fasta sequence file.
IndexedFastaSequenceFile(java.io.File file, FastaSequenceIndex index) Open the given indexed fasta sequence file.
IndexedFastaSequenceFile(java.nio.file.Path path) Open the given indexed fasta sequence file.
IndexedFastaSequenceFile(java.nio.file.Path path, FastaSequenceIndex index) Open the given indexed fasta sequence file.

Method Summary

Modifier and Type	Method and Description
static boolean	canCreateIndexedFastaReader(java.io.File fastaFile)
static boolean	canCreateIndexedFastaReader(java.nio.file.Path fastaFile)
void	close()
protected static java.io.File	findSequenceDictionary(java.io.File file)
protected static java.nio.file.Path	findSequenceDictionary(java.nio.file.Path path)
protected java.lang.String	getAbsolutePath() Returns the full path to the reference file.
protected java.nio.file.Path	getPath() Returns the path to the reference file.
ReferenceSequence	getSequence(java.lang.String contig) Retrieves the complete sequence described by this contig.
SAMSequenceDictionary	getSequenceDictionary() Retrieves the sequence dictionary for the fasta file.
ReferenceSequence	getSubsequenceAt(java.lang.String contig, long start, long stop) Gets the subsequence of the contig in the range [start,stop]
boolean	isIndexed() default implementation -- override if index is supported
ReferenceSequence	nextSequence() Gets the next sequence if available, or null if not present.
void	reset() Reset the iterator over the index.
protected static void	sanityCheckDictionaryAgainstIndex(java.lang.String fastaFile, SAMSequenceDictionary sequenceDictionary, FastaSequenceIndex index) Do some basic checking to make sure the dictionary and the index match.
java.lang.String	toString() A simple toString implementation for debugging.

Methods inherited from class java.lang.Object

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

Field Detail

sequenceDictionary

protected SAMSequenceDictionary sequenceDictionary

Constructor Detail

IndexedFastaSequenceFile

public IndexedFastaSequenceFile(java.io.File file,
                                FastaSequenceIndex index)

Open the given indexed fasta sequence file. Throw an exception if the file cannot be opened.

Parameters:

file - The file to open.

index - Pre-built FastaSequenceIndex, for the case in which one does not exist on disk.

Throws:

java.io.FileNotFoundException - If the fasta or any of its supporting files cannot be found.

IndexedFastaSequenceFile

public IndexedFastaSequenceFile(java.io.File file)
                         throws java.io.FileNotFoundException

Open the given indexed fasta sequence file. Throw an exception if the file cannot be opened.

Parameters:

file - The file to open.

Throws:

java.io.FileNotFoundException - If the fasta or any of its supporting files cannot be found.

IndexedFastaSequenceFile

public IndexedFastaSequenceFile(java.nio.file.Path path,
                                FastaSequenceIndex index)

Open the given indexed fasta sequence file. Throw an exception if the file cannot be opened.

Parameters:

path - The file to open.

index - Pre-built FastaSequenceIndex, for the case in which one does not exist on disk.

IndexedFastaSequenceFile

public IndexedFastaSequenceFile(java.nio.file.Path path)
                         throws java.io.FileNotFoundException

Open the given indexed fasta sequence file. Throw an exception if the file cannot be opened.

Parameters:

path - The file to open.

Throws:

java.io.FileNotFoundException - If the fasta or any of its supporting files cannot be found.

Method Detail

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.

canCreateIndexedFastaReader

public static boolean canCreateIndexedFastaReader(java.io.File fastaFile)

canCreateIndexedFastaReader

public static boolean canCreateIndexedFastaReader(java.nio.file.Path fastaFile)

sanityCheckDictionaryAgainstIndex

protected static void sanityCheckDictionaryAgainstIndex(java.lang.String fastaFile,
                                                        SAMSequenceDictionary sequenceDictionary,
                                                        FastaSequenceIndex index)

Do some basic checking to make sure the dictionary and the index match.

Parameters:

fastaFile - Used for error reporting only.

sequenceDictionary - sequence dictionary to check against the index.

index - index file to check against the dictionary.

getSequenceDictionary

public SAMSequenceDictionary getSequenceDictionary()

Retrieves the sequence dictionary for the fasta file.

Specified by:

getSequenceDictionary in interface ReferenceSequenceFile

Returns:

sequence dictionary of the fasta.

getSequence

public ReferenceSequence getSequence(java.lang.String contig)

Retrieves the complete sequence described by this contig.

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(java.lang.String contig,
                                          long start,
                                          long stop)

Gets the subsequence of the contig in the range [start,stop]

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.

nextSequence

public ReferenceSequence nextSequence()

Gets the next sequence if available, or null if not present.

Specified by:

nextSequence in interface ReferenceSequenceFile

Returns:

next sequence if available, or null if not present.

reset

public void reset()

Reset the iterator over the index.

Specified by:

reset in interface ReferenceSequenceFile

toString

public java.lang.String toString()

A simple toString implementation for debugging.

Specified by:

toString in interface ReferenceSequenceFile

Returns:

String representation of the file.

close

public void close()
           throws java.io.IOException

Specified by:

close in interface ReferenceSequenceFile

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Throws:

java.io.IOException

findSequenceDictionary

protected static java.io.File findSequenceDictionary(java.io.File file)

findSequenceDictionary

protected static java.nio.file.Path findSequenceDictionary(java.nio.file.Path path)

getPath

protected java.nio.file.Path getPath()

Returns the path to the reference file.

getAbsolutePath

protected java.lang.String getAbsolutePath()

Returns the full path to the reference file.