cabal-version:  2.2
name:           BiobaseFasta
version:        0.4.0.1
author:         Christian Hoener zu Siederdissen
maintainer:     choener@bioinf.uni-leipzig.de
homepage:       https://github.com/choener/BiobaseFasta
bug-reports:    https://github.com/choener/BiobaseFasta/issues
copyright:      Christian Hoener zu Siederdissen, 2011-2021
category:       Bioinformatics
license:        BSD-3-Clause
license-file:   LICENSE
build-type:     Simple
stability:      experimental
tested-with:    GHC == 8.8.4, GHC == 8.10.4, GHC == 9.0
synopsis:       streaming FASTA parser
description:
                Stream-based handling of FASTA files. The user selects a window
                size, the library then handles the window. For each window, the
                previous (past) window is available, in case some data sits on
                the boundary between windows.
                .
                Greg Schwartz' <http://hackage.haskell.org/package/fasta>
                package is a lot more complete. This one is mostly tailored to
                my usage requirements (and may at some point use his library).



extra-source-files:
  changelog.md
  README.md
  tests/sample1.fa
  tests/sample2.fa
  tests/sample3.fa



common deps
  build-depends: base                 >= 4.7    && < 5.0
               , bytestring
               , lens                 >= 4.0
               , resourcet            >= 1.0
               , streaming            >= 0.1
               , streaming-bytestring >= 0.2
               , string-conversions   >= 0.4
               --
               , BiobaseTypes         == 0.2.1.*
               , DPutils              == 0.1.1.*
  default-language:
    Haskell2010
  default-extensions: BangPatterns
                    , DataKinds
                    , DeriveDataTypeable
                    , DeriveGeneric
                    , FlexibleContexts
                    , FlexibleInstances
                    , GADTs
                    , GeneralizedNewtypeDeriving
                    , KindSignatures
                    , LambdaCase
                    , MultiParamTypeClasses
                    , MultiWayIf
                    , NoMonomorphismRestriction
                    , OverloadedStrings
                    , PolyKinds
                    , RankNTypes
                    , RecordWildCards
                    , ScopedTypeVariables
                    , TemplateHaskell
                    , TypeApplications
                    , TypeFamilies
                    , UnicodeSyntax
                    , ViewPatterns
  ghc-options:
    -O2

library
  import:
    deps
  exposed-modules:
    Biobase.Fasta.Streaming
    Biobase.Fasta.Strict



-- | A simple tool for fasta files, showing some features

executable fastaextract
  import: deps
  build-depends: base
               , optparse-applicative >= 0.14
               --
               , BiobaseFasta
  hs-source-dirs:
    src
  main-is:
    fastaextract.hs
  ghc-options:
    -rtsopts



test-suite properties
  import:
    deps
  type:
    exitcode-stdio-1.0
  main-is:
    properties.hs
  ghc-options:
    -threaded -rtsopts -with-rtsopts=-N
  hs-source-dirs:
    tests
  build-depends: QuickCheck
               , filepath
               , tasty                  >= 0.11
               , tasty-hunit            >= 0.9
               , tasty-golden           >= 2.3
               , tasty-quickcheck       >= 0.8
               , tasty-silver           >= 3.1.9
               , tasty-th               >= 0.1
               , text
               --
               , BiobaseFasta



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