name:           BiobaseInfernal
version:        0.7.0.0
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:  >= 1.6.0
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 0.7.0.0
                .
                * work-in-progress release (some features missing)
                .
                * working CM parsing
                .
                * type defns have changed. using phantom types to specify what kind of model we are working with
                .
                * using conduit instead of iteratee



extra-source-files:

library
  build-depends:
    base >3 && <5,
    attoparsec          == 0.10.*   ,
    attoparsec-conduit  == 0.5.*    ,
    biocore             == 0.2      ,
    bytestring                      ,
    bytestring-lexing   == 0.4.*    ,
    conduit             == 0.5.*    ,
    containers,
    either-unwrap       == 1.1      ,
    lens                == 3.*      ,
    primitive           >= 0.5      ,
    transformers        == 0.3.*    ,
    tuple               == 0.2.*    ,
    vector              >= 0.10     ,
    BiobaseXNA          == 0.6.3.*  ,
    PrimitiveArray      == 0.4.0.0

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

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

source-repository head
  type: git
  location: git://github.com/choener/BiobaseInfernal