Class FastaSequenceIndexCreator

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

public final class FastaSequenceIndexCreator extends Object
Static methods to create an FastaSequenceIndex.
  • Method Details

    • 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, SAMException
      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.