Class FastaSequenceIndexCreator

    • 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.