java.lang.Object
- htsjdk.samtools.reference.IndexedFastaSequenceFile

All Implemented Interfaces:

ReferenceSequenceFile, Closeable, AutoCloseable
```
public class IndexedFastaSequenceFile
extends Object
```
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.

Constructor Summary

Constructors
Constructor	Description
`IndexedFastaSequenceFile(File file)`	Open the given indexed fasta sequence file.
`IndexedFastaSequenceFile(File file, FastaSequenceIndex index)`	Open the given indexed fasta sequence file.
`IndexedFastaSequenceFile(String source, SeekableStream in, FastaSequenceIndex index, SAMSequenceDictionary dictionary)`	Initialise the given indexed fasta sequence file stream.
`IndexedFastaSequenceFile(Path path)`	Open the given indexed fasta sequence file.
`IndexedFastaSequenceFile(Path path, FastaSequenceIndex index)`	Open the given indexed fasta sequence file.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`static boolean`	`canCreateIndexedFastaReader(File fastaFile)`	Deprecated. use `ReferenceSequenceFileFactory.canCreateIndexedFastaReader(Path)` instead.
`static boolean`	`canCreateIndexedFastaReader(Path fastaFile)`	Deprecated. use `ReferenceSequenceFileFactory.canCreateIndexedFastaReader(Path)` instead.
`void`	`close()`
`protected SAMSequenceDictionary`	`findAndLoadSequenceDictionary(Path fasta)`	Attempts to find and load the sequence dictionary if present.
`protected static Path`	`findFastaIndex(Path fastaFile)`
`protected static Path`	`findRequiredFastaIndexFile(Path fastaFile)`
`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.
`FastaSequenceIndex`	`getIndex()`
`protected Path`	`getPath()`	Returns the path to the reference file.
`ReferenceSequence`	`getSequence(String contig)`	Retrieves the complete sequence described by this contig.
`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)`	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.
`protected int`	`readFromPosition(ByteBuffer buffer, long position)`	Reads a sequence of bytes from this channel into the given buffer, starting at the given file position.
`void`	`reset()`	Reset the iterator over the index.
`protected static void`	`sanityCheckDictionaryAgainstIndex(String fastaFile, SAMSequenceDictionary sequenceDictionary, FastaSequenceIndex index)`	Do some basic checking to make sure the dictionary and the index match.
`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 Detail
  - IndexedFastaSequenceFile
```
public IndexedFastaSequenceFile(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:
    
    FileNotFoundException - If the fasta or any of its supporting files cannot be found.
  - IndexedFastaSequenceFile
```
public IndexedFastaSequenceFile(File file)
                         throws FileNotFoundException
```
    Open the given indexed fasta sequence file. Throw an exception if the file cannot be opened.
    
    Parameters:
    
    file - The file to open.
    
    Throws:
    
    FileNotFoundException - If the fasta or any of its supporting files cannot be found.
  - IndexedFastaSequenceFile
```
public IndexedFastaSequenceFile(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(Path path)
                         throws FileNotFoundException
```
    Open the given indexed fasta sequence file. Throw an exception if the file cannot be opened.
    
    Parameters:
    
    path - The file to open.
    
    Throws:
    
    FileNotFoundException - If the fasta or any of its supporting files cannot be found.
  - IndexedFastaSequenceFile
```
public IndexedFastaSequenceFile(String source,
                                SeekableStream in,
                                FastaSequenceIndex index,
                                SAMSequenceDictionary dictionary)
```
    Initialise the given indexed fasta sequence file stream.
    
    Parameters:
    
    source - The named source of the reference file (used in error messages).
    
    in - The input stream to read the fasta file from.
    
    index - The fasta index.
    
    dictionary - The sequence dictionary, or null if there isn't one.
- Method Detail
  - canCreateIndexedFastaReader
```
@Deprecated
public static boolean canCreateIndexedFastaReader(File fastaFile)
```
    Deprecated.
    use ReferenceSequenceFileFactory.canCreateIndexedFastaReader(Path) instead.
  - canCreateIndexedFastaReader
```
@Deprecated
public static boolean canCreateIndexedFastaReader(Path fastaFile)
```
    Deprecated.
    use ReferenceSequenceFileFactory.canCreateIndexedFastaReader(Path) instead.
  - readFromPosition
```
protected int readFromPosition(ByteBuffer buffer,
                               long position)
                        throws IOException
```
    Reads a sequence of bytes from this channel into the given buffer, starting at the given file position.
    
    Parameters:
    
    buffer - the buffer into which bytes are to be transferred
    
    position - the position to start reading at
    
    Returns:
    
    the number of bytes read
    
    Throws:
    
    IOException - if an I/O error occurs while reading
  - close
```
public void close()
           throws IOException
```
    Throws:
    
    IOException
  - findRequiredFastaIndexFile
```
protected static Path findRequiredFastaIndexFile(Path fastaFile)
                                          throws FileNotFoundException
```
    Throws:
    
    FileNotFoundException
  - findFastaIndex
```
protected static Path findFastaIndex(Path fastaFile)
```
  - sanityCheckDictionaryAgainstIndex
```
protected static void sanityCheckDictionaryAgainstIndex(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.
  - getIndex
```
public FastaSequenceIndex getIndex()
```
  - nextSequence
```
public ReferenceSequence nextSequence()
```
    Gets the next sequence if available, or null if not present.
    
    Returns:
    
    next sequence if available, or null if not present.
  - reset
```
public void reset()
```
    Reset the iterator over the index.
  - isIndexed
```
public final 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)
```
    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(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.
  - 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.

Class IndexedFastaSequenceFile

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

IndexedFastaSequenceFile

IndexedFastaSequenceFile

IndexedFastaSequenceFile

IndexedFastaSequenceFile

IndexedFastaSequenceFile

Method Detail

canCreateIndexedFastaReader

canCreateIndexedFastaReader

readFromPosition

close

findRequiredFastaIndexFile

findFastaIndex

sanityCheckDictionaryAgainstIndex

getIndex

nextSequence

reset

isIndexed

getSequence

getSubsequenceAt

findAndLoadSequenceDictionary

findSequenceDictionary

findSequenceDictionary

getPath

getSource

getSequenceDictionary

getAbsolutePath

toString