name:           BiobaseInfernal
version:        0.8.1.0
author:         Christian Hoener zu Siederdissen
maintainer:     choener@bioinf.uni-leipzig.de
homepage:       https://github.com/choener/BiobaseInfernal
bug-reports:    https://github.com/choener/BiobaseInfernal/issues
copyright:      Christian Hoener zu Siederdissen, 2011 - 2017
category:       Bioinformatics
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.10.0
tested-with:    GHC == 7.10.3, GHC == 8.0.1
synopsis:       Infernal data structures and tools
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.
                .
                The @cmsearchFilter@ program provides filtering and coloring
                options.



extra-source-files:
  changelog.md
  README.md



library
  build-depends: base                 >= 4.7      &&  < 5.0
               , aeson                >= 0.9
               , attoparsec           >= 0.12
               , binary               >= 0.7
               , bytestring
               , cereal               >= 0.4
               , cereal-text          >= 0.1
               , cereal-vector        >= 0.2
               , containers
               , data-default         >= 0.5
               , deepseq              >= 1.4
               , filepath             >= 1.3
               , hashable             >= 1.2
               , lens                 >= 4.0
               , parallel             >= 3.0
               , pipes                >= 4.0
               , pipes-attoparsec     >= 0.5
               , pipes-bytestring     >= 2.0
               , pipes-parse          >= 3.0
               , pipes-safe           >= 2.2
               , pipes-zlib           >= 0.4
               , primitive            >= 0.5
               , strict               >= 0.3
               , string-conversions   >= 0.4
               , text                 >= 1.0
               , text-binary          >= 0.1
               , transformers
               , tuple                >= 0.3
               , unordered-containers >= 0.2
               , utf8-string          >= 1.0
               , vector               >= 0.10
               , vector-th-unbox      >= 0.2
               , zlib                 >= 0.6
               -- own libraries (keep tight control over versioning?)
               , BiobaseTypes         == 0.1.2.*
               , BiobaseXNA           == 0.9.3.*
               , DPutils              == 0.0.1.*
               , PrimitiveArray       == 0.8.0.*

  exposed-modules:
    Biobase.SElab.Model
    Biobase.SElab.Model.Import
    Biobase.SElab.Model.Types
    Biobase.SElab.CM
    Biobase.SElab.CM.Import
    Biobase.SElab.CM.ModelStructure
    Biobase.SElab.CM.Types
    Biobase.SElab.Common.Parser
    Biobase.SElab.HMM
    Biobase.SElab.HMM.Import
    Biobase.SElab.HMM.Types
    Biobase.SElab.Taxonomy
    Biobase.SElab.Taxonomy.Import
  default-language:
    Haskell2010
  default-extensions: BangPatterns
                    , DataKinds
                    , DeriveGeneric
                    , FlexibleContexts
                    , FlexibleInstances
                    , GADTs
                    , GeneralizedNewtypeDeriving
                    , LambdaCase
                    , MultiParamTypeClasses
                    , MultiWayIf
                    , OverloadedStrings
                    , ParallelListComp
                    , PatternSynonyms
                    , RankNTypes
                    , RecordWildCards
                    , ScopedTypeVariables
                    , TemplateHaskell
                    , TupleSections
                    , TypeFamilies
                    , TypeOperators
                    , TypeSynonymInstances
                    , UndecidableInstances
  ghc-options:
    -O2 -funbox-strict-fields



-- provides advanced cmsearch hit filtering functionality.

executable cmsearchFilter
  build-depends: base
               , cmdargs          >= 0.10
               --
               , BiobaseInfernal
  hs-source-dirs:
    src
  main-is:
    cmsearchFilter.hs
  default-language:
    Haskell2010
  ghc-options:
    -O2



benchmark parsing
  type:
    exitcode-stdio-1.0
  build-depends: base
               , criterion        >= 1.1.0.0
               , lens
               , text
               , transformers
               --
               , BiobaseInfernal
  hs-source-dirs:
    tests
  main-is:
    parsing.hs
  default-language:
    Haskell2010
  ghc-options:
    -O2 -threaded -rtsopts "-with-rtsopts=-N -I0"



test-suite properties
  type:
    exitcode-stdio-1.0
  main-is:
    properties.hs
  ghc-options:
    -threaded -rtsopts -with-rtsopts=-N
  hs-source-dirs:
    tests
  default-language:
    Haskell2010
  default-extensions: OverloadedStrings
                    , ScopedTypeVariables
                    , TemplateHaskell
  build-depends: base
               , HUnit              >= 1.2
               , lens
               , QuickCheck
               , tasty              >= 0.11
               , tasty-hunit        >= 0.9
               , tasty-quickcheck   >= 0.8
               , tasty-th           >= 0.1
               --
               , BiobaseInfernal



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