htsjdk.samtools.reference

Class BlockCompressedIndexedFastaSequenceFile

java.lang.Object

htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile

All Implemented Interfaces:

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

public class BlockCompressedIndexedFastaSequenceFile
extends java.lang.Object

A block-compressed FASTA file driven by an index for fast lookups.

Supports two interfaces: the ReferenceSequenceFile for old-style, stateful lookups and a direct getter.

Constructor Summary

Constructors

Constructor and Description
BlockCompressedIndexedFastaSequenceFile(java.nio.file.Path path)
BlockCompressedIndexedFastaSequenceFile(java.nio.file.Path path, FastaSequenceIndex index)
BlockCompressedIndexedFastaSequenceFile(java.nio.file.Path path, FastaSequenceIndex index, GZIIndex gziIndex)
BlockCompressedIndexedFastaSequenceFile(java.lang.String source, SeekableStream in, FastaSequenceIndex index, SAMSequenceDictionary dictionary, GZIIndex gziIndex) Initialize the given indexed fasta sequence file stream.

Method Summary

Modifier and Type	Method and Description
void	close()
protected SAMSequenceDictionary	findAndLoadSequenceDictionary(java.nio.file.Path fasta) Attempts to find and load the sequence dictionary if present.
protected static java.nio.file.Path	findFastaIndex(java.nio.file.Path fastaFile)
protected static java.nio.file.Path	findRequiredFastaIndexFile(java.nio.file.Path fastaFile)
protected static java.io.File	findSequenceDictionary(java.io.File file) Deprecated. use findSequenceDictionary(Path) instead.
protected static java.nio.file.Path	findSequenceDictionary(java.nio.file.Path fastaPath) Attempts to locate the sequence dictionary file adjacent to the reference fasta file.
protected java.lang.String	getAbsolutePath() Returns the full path to the reference file.
FastaSequenceIndex	getIndex()
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() Returns the list of sequence records associated with the reference sequence if found otherwise null.
protected java.lang.String	getSource() Returns the named source of the reference 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.
protected int	readFromPosition(java.nio.ByteBuffer buffer, long position) Reads a sequence of bytes from this sequence file into the given buffer, starting at the given file position.
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() 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

BlockCompressedIndexedFastaSequenceFile

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

Throws:

java.io.FileNotFoundException

BlockCompressedIndexedFastaSequenceFile

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

BlockCompressedIndexedFastaSequenceFile

public BlockCompressedIndexedFastaSequenceFile(java.nio.file.Path path,
                                               FastaSequenceIndex index,
                                               GZIIndex gziIndex)

BlockCompressedIndexedFastaSequenceFile

public BlockCompressedIndexedFastaSequenceFile(java.lang.String source,
                                               SeekableStream in,
                                               FastaSequenceIndex index,
                                               SAMSequenceDictionary dictionary,
                                               GZIIndex gziIndex)

Initialize 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; should not be decompressed already.

index - The fasta index.

dictionary - The sequence dictionary, or null if there isn't one.

gziIndex - The GZI index; may not be null.

Method Detail

readFromPosition

protected int readFromPosition(java.nio.ByteBuffer buffer,
                               long position)
                        throws java.io.IOException

Reads a sequence of bytes from this sequence file 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:

java.io.IOException - if an I/O error occurs while reading

close

public void close()
           throws java.io.IOException

Throws:

java.io.IOException

findRequiredFastaIndexFile

protected static java.nio.file.Path findRequiredFastaIndexFile(java.nio.file.Path fastaFile)
                                                        throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

findFastaIndex

protected static java.nio.file.Path findFastaIndex(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.

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(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.

findAndLoadSequenceDictionary

protected SAMSequenceDictionary findAndLoadSequenceDictionary(java.nio.file.Path fasta)

Attempts to find and load the sequence dictionary if present.

findSequenceDictionary

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

Deprecated. use findSequenceDictionary(Path) instead.

findSequenceDictionary

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

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

getPath

protected java.nio.file.Path getPath()

Returns the path to the reference file.

getSource

protected java.lang.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 java.lang.String getAbsolutePath()

Returns the full path to the reference file.

toString

public java.lang.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 java.lang.Object

Returns:

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