name:           BiobaseInfernal
version:        0.6.0.1
author:         Christian Hoener zu Siederdissen
maintainer:     choener@tbi.univie.ac.at
homepage:       http://www.tbi.univie.ac.at/~choener/
copyright:      Christian Hoener zu Siederdissen, 2011
category:       Bioinformatics
synopsis:       Infernal data structures and tools
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.4.0
description:
                Provides import and export facilities for Infernal/Rfam data
                formats. We include Stockholm, CM, verbose Infernal results,
                and tabulated Infernal results. Some small tools are included.
                .
                The VerboseHit format is slightly extended to allow simple
                annotations. This extension should be backward-compatible with
                standard-compliant parsers.
                .
                This package uses Int's to store sequence position information.
                Don't compile for 32bit. (And yes, this is a TODO, to change to
                Int64).
                .
                .
                .
                Changes in 0.6.0.1
                .
                * haddock should finish now
                .
                Changes in 0.6.0.0
                .
                * multiple changes to data representation (mostly newtypes) and
                  documentation
                .
                * load the Rfam.fasta.gz file (and prepare lookup structures)
                .
                * partial biocore integration

extra-source-files:

library
  build-depends:
    base >3 && <5,
    biocore,
    attoparsec,
    attoparsec-iteratee,
    bytestring,
    containers,
    either-unwrap,
    iteratee,
    iteratee-compress,
    transformers,
    tuple,
    vector,
    PrimitiveArray

  exposed-modules:
    Biobase.Infernal
    Biobase.Infernal.Clan
    Biobase.Infernal.Clan.Import
    Biobase.Infernal.CM
    Biobase.Infernal.CM.Export
    Biobase.Infernal.CM.Import
    Biobase.Infernal.Hit
    Biobase.Infernal.RfamFasta
    Biobase.Infernal.RfamFasta.Import
    Biobase.Infernal.TabularHit
    Biobase.Infernal.TabularHit.Import
    Biobase.Infernal.Taxonomy
    Biobase.Infernal.Taxonomy.Import
    Biobase.Infernal.Types
    Biobase.Infernal.VerboseHit
    Biobase.Infernal.VerboseHit.Export
    Biobase.Infernal.VerboseHit.Import
    Biobase.Infernal.VerboseHit.Internal

  ghc-options:
    -O2 -funbox-strict-fields