    {- |
       This is a meta-module importing and re-exporting sequence-related stuff.

       It encompasses the "Bio.Sequence.SeqData", "Bio.Sequence.Fasta", and "Bio.Sequence.TwoBit" modules.
    -}

    module Bio.Sequence
        (
        -- * Data structures etc ("Bio.Sequence.SeqData")
          Sequence(..), Unknown, Offset, SeqData, Qual, QualData
        -- ** Accessor functions
        , seqlength, seqlabel, seqheader, seqdata, seqqual, (!)
        , appendHeader, setHeader

        -- ** Converting to and from String.
        , fromStr, toStr
        -- ** Nucleotide functionality.
        , compl, revcompl, revcompl', Nuc, castToNuc
        -- ** Protein sequence functionality
        , Amino(..), translate, fromIUPAC, toIUPAC, castToAmino
        -- ** Other utility functions
        , defragSeq, seqmap

        -- * File formats
        -- ** The Fasta file format ("Bio.Sequence.Fasta")
        , readFasta, hReadFasta
        , writeFasta, hWriteFasta
        -- ** Quality data
        -- | Not part of the Fasta format, and treated separately.
        , readQual, writeQual, hWriteQual
        , readFastaQual
        , writeFastaQual, hWriteFastaQual

        -- ** The FastQ format ("Bio.Sequence.FastQ")
        -- Combines sequence data and quality in one file.
        -- Warning: Solexa uses a different formula for the quality values!
        , readFastQ, writeFastQ, hReadFastQ, hWriteFastQ

        -- ** The phd file format ("Bio.Sequence.Phd")
        -- | These contain base (nucleotide) calling information,
        --   and are generated by @phred@.
        , readPhd, hReadPhd

        -- ** TwoBit file format support ("Bio.Seqeunce.TwoBit")
        -- | Used by @BLAT@ and related tools.
        , decode2Bit, read2Bit, hRead2Bit
        -- ,encode2Bit, write2Bit, hWrite2Bit

        -- * Hashing functionality ("Bio.Sequence.HashWord")
        -- | Packing words from sequences into integral data types
        , HashF (..)
        , contigous, rcontig, rcpacked

        -- * Entropy calculations
        , KWords(..), entropy
        ) where

    -- basic sequence data structures
    import Bio.Sequence.SeqData

    -- file formats
    import Bio.Sequence.Fasta
    import Bio.Sequence.FastQ
    import Bio.Sequence.Phd
    import Bio.Sequence.TwoBit

    -- sequence-oriented stuff
    import Bio.Sequence.Entropy
    import Bio.Sequence.HashWord