# fai

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# Imports

hts_concat, utils

# Types

    Fai = ref object
      cptr*: ptr faidx_t

  Fai provides random access to fasta sequences.

# Procs

    proc open(fai: var Fai; path: string): bool {...}{.raises: [IOError], tags: [WriteIOEffect].}

  open an fai and return a bool indicating success

    proc len(fai: Fai): int {...}{.inline, raises: [], tags: [].}

  the number of sequences in the index.

    proc chrom_len(fai: Fai; chrom: string): int {...}{.raises: [ValueError], tags: [].}

  return the length of the requested chromosome.

    proc `[]`(fai: Fai; i: int): string {...}{.inline, raises: [], tags: [].}

  return the name of the i'th sequence.

    proc cget(fai: Fai; region: string; start: int = 0; stop: int = 0): cstring {...}{.inline,
        raises: [KeyError, IOError], tags: [WriteIOEffect].}

  get the sequence for the specified region (chr1:10-20) or chromosome and start, end, e.g. "chr1", 9, 20 the user is responsible for freeing the result.

    proc get(fai: Fai; region: string; start: int = 0; stop: int = 0): string {...}{.
        raises: [KeyError, IOError], tags: [WriteIOEffect].}

  get the sequence for the specified region (chr1:10-20) or chromosome and start, end, e.g. "chr1", 9, 20