public final class FastaSequenceIndexCreator extends Object
FastaSequenceIndex
.Modifier and Type | Method | Description |
---|---|---|
static FastaSequenceIndex |
buildFromFasta(Path fastaFile) |
Builds a FastaSequenceIndex on the fly from a FASTA file.
|
static void |
create(Path fastaFile,
boolean overwrite) |
Creates a FASTA .fai index for the provided FASTA.
|
public static void create(Path fastaFile, boolean overwrite) throws IOException
fastaFile
- the file to build the index from.overwrite
- if the .fai index already exists override it if true
; otherwise, throws a SAMException
.SAMException
- if the fai file already exists or the file is malformed.IOException
- if an IO error occurs.public static FastaSequenceIndex buildFromFasta(Path fastaFile) throws IOException
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)
.
fastaFile
- the FASTA file.SAMException
- for formatting errors.IOException
- if an IO error occurs.