cabal-version: >=1.10
name: sequenceTools
version: 1.4.0.5
license: GPL-3
license-file: LICENSE
maintainer: stephan.schiffels@mac.com
author: Stephan Schiffels
synopsis: A package with tools for processing DNA sequencing data
description:
    The tools in this package process sequencing Data, in particular from ancient DNA sequencing libraries. Key tool in this package is pileupCaller, a tool to randomly sample genotypes from sequencing data.
category: Bioinformatics
build-type: Simple
extra-source-files:
    README.md
    Changelog.md

library
    exposed-modules:
        SequenceTools.Utils
        SequenceTools.PileupCaller
    hs-source-dirs: src
    other-modules:
        Paths_sequenceTools
    default-language: Haskell2010
    build-depends:
        base >=4.7 && <5,
        optparse-applicative >=0.14.3.0,
        random >=1.1,
        sequence-formats >=1.4.1,
        bytestring >=0.10.8.2,
        vector >=0.12.0.3,
        pipes >=4.3.11

executable pileupCaller
    main-is: pileupCaller.hs
    hs-source-dirs: src-executables
    default-language: Haskell2010
    ghc-options: -threaded -rtsopts -with-rtsopts=-N2
    build-depends:
        base >=4.12.0.0,
        sequenceTools -any,
        sequence-formats >=1.4.1,
        optparse-applicative >=0.14.3.0,
        pipes >=4.3.11,
        rio >=0.1.11.0,
        vector >=0.12.0.3,
        random >=1.1,
        bytestring >=0.10.8.2,
        pipes-safe >=2.3.1,
        pipes-ordered-zip >=1.1.0,
        split >=0.2.3.3,
        ansi-wl-pprint >=0.6.9

executable vcf2eigenstrat
    main-is: vcf2eigenstrat.hs
    hs-source-dirs: src-executables
    default-language: Haskell2010
    build-depends:
        base >=4.12.0.0,
        sequenceTools -any,
        pipes-ordered-zip >=1.1.0,
        sequence-formats >=1.4.1,
        bytestring >=0.10.8.2,
        vector >=0.12.0.3,
        optparse-applicative >=0.14.3.0,
        pipes >=4.3.11,
        pipes-safe >=2.3.1

executable genoStats
    main-is: genoStats.hs
    hs-source-dirs: src-executables
    default-language: Haskell2010
    build-depends:
        base >=4.12.0.0,
        sequence-formats >=1.4.1,
        sequenceTools -any,
        foldl >=1.4.5,
        bytestring >=0.10.8.2,
        vector >=0.12.0.3,
        lens-family >=1.2.3,
        optparse-applicative >=0.14.3.0,
        pipes >=4.3.11,
        pipes-group >=1.0.12,
        pipes-safe >=2.3.1

test-suite sequenceToolsTests
    type: exitcode-stdio-1.0
    main-is: Spec.hs
    hs-source-dirs: test
    other-modules:
        SequenceTools.UtilsSpec
        SequenceTools.PileupCallerSpec
    default-language: Haskell2010
    build-depends:
        base >=4.12.0.0,
        hspec >=2.7.1,
        sequenceTools -any,
        sequence-formats >=1.4.1,
        vector >=0.12.0.3,
        bytestring >=0.10.8.2,
        pipes >=4.3.11