htsjdk.samtools.reference

Class FastaSequenceIndexCreator

java.lang.Object

htsjdk.samtools.reference.FastaSequenceIndexCreator

public final class FastaSequenceIndexCreator
extends java.lang.Object

Static methods to create an FastaSequenceIndex.

Method Summary

Modifier and Type	Method and Description
static FastaSequenceIndex	buildFromFasta(java.nio.file.Path fastaFile) Builds a FastaSequenceIndex on the fly from a FASTA file.
static void	create(java.nio.file.Path fastaFile, boolean overwrite) Creates a FASTA .fai index for the provided FASTA.

Methods inherited from class java.lang.Object

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

Method Detail

create

public static void create(java.nio.file.Path fastaFile,
                          boolean overwrite)
                   throws java.io.IOException

Creates a FASTA .fai index for the provided FASTA.

Parameters:

fastaFile - the file to build the index from.

overwrite - if the .fai index already exists override it if true; otherwise, throws a SAMException.

Throws:

SAMException - if the fai file already exists or the file is malformed.

java.io.IOException - if an IO error occurs.

buildFromFasta

public static FastaSequenceIndex buildFromFasta(java.nio.file.Path fastaFile)
                                         throws java.io.IOException

Builds a FastaSequenceIndex on the fly from a FASTA file.

Note: this also allows to create an index for a compressed file, but does not generate the .gzi index required for use it with samtools. To generate that index, use GZIIndex.buildIndex(Path).

Parameters:

fastaFile - the FASTA file.

Returns:

a fai index.

Throws:

SAMException - for formatting errors.

java.io.IOException - if an IO error occurs.