name:           BiobaseBlast
version:        0.2.1.0
author:         Christian Hoener zu Siederdissen, Florian Eggenhofer
maintainer:     choener@bioinf.uni-leipzig.de
homepage:       https://github.com/choener/BiobaseBlast
bug-reports:    https://github.com/choener/BiobaseBlast/issues
copyright:      Christian Hoener zu Siederdissen, 2013 - 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, GHC == 8.0.2
synopsis:       BLAST-related tools
description:
                This library contains BLAST-related functionality:
                .
                - Parser for tabular NCBI BLAST+ output
                - Parsers for BLOSUM and PAM matrices.
                - Specialized substitution functions for (in)complete amino
                  acid / nucleotide triplet substitution.
                - Incomplete nucleotide patterns map one or two nucleotides to
                  an amino acid (need for indel editing in the mitochondria of
                  certain species like /p.polycephalum/).
                .
                The matrices are currently not provided but can be found here:
                <ftp://ftp.ncbi.nih.gov/blast/matrices/>



extra-source-files:
  changelog.md
  README.md
  tests/succeed/*.golden
  tests/succeed/*.test

library
  build-depends: base             >= 4.7      && < 5.0
               , aeson            >= 1.0
               , attoparsec       >= 0.13
               , binary           >= 0.7
               , bytestring
               , cereal           >= 0.4
               , containers
               , deepseq          >= 1.3
               , directory
               , vector           >= 0.10
               , vector-th-unbox  >= 0.2
               --
               , BiobaseTypes     == 0.1.2.*
               , BiobaseXNA       == 0.9.3.*
               , PrimitiveArray   == 0.8.0.*

  default-language:
    Haskell2010
  default-extensions: DeriveGeneric
                    , MultiParamTypeClasses
                    , TemplateHaskell
                    , TypeFamilies
                    , TypeOperators
  exposed-modules:
    Biobase.SubstMatrix
    Biobase.SubstMatrix.Import
    Biobase.BLAST
    Biobase.BLAST.Import
    Biobase.BLAST.Types

  ghc-options:
    -O2



test-suite properties
  type:
    exitcode-stdio-1.0
  main-is:
    properties.hs
  ghc-options:
    -O2 -threaded -rtsopts -with-rtsopts=-N
  hs-source-dirs:
    tests
  default-language:
    Haskell2010
  default-extensions: BangPatterns
                    , OverloadedStrings
                    , ScopedTypeVariables
                    , TemplateHaskell
  build-depends: base
               , bytestring
               , containers
               , filepath
               , split                      >= 0.2.3
               , tasty                      >= 0.11
               , tasty-quickcheck           >= 0.8
               , tasty-silver               >= 3.1.9
               , tasty-th                   >= 0.1
               , text
               --
               , BiobaseBlast



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

source-repository this
  type:     git
  location: https://github.com/choener/BiobaseBlast/tree/0.2.1.0
  tag:      0.2.1.0