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.