FastaSequenceIndexCreator (htsjdk 2.23.0 API)

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

public final class FastaSequenceIndexCreator
extends Object

Static methods to create an FastaSequenceIndex.

Method Summary

All Methods Static Methods Concrete Methods
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.

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(Path fastaFile,
                          boolean overwrite)
                   throws 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.
    
    IOException - if an IO error occurs.
  - buildFromFasta
```
public static FastaSequenceIndex buildFromFasta(Path fastaFile)
                                         throws 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.
    
    IOException - if an IO error occurs.