cabal-version: >=1.10
name: sequence-formats
version: 1.4.1
x-revision: 1
license: GPL-3
license-file: LICENSE
maintainer: stephan.schiffels@mac.com
author: Stephan Schiffels
synopsis: A package with basic parsing utilities for several Bioinformatic data formats.
description:
    Contains utilities to parse and write Eigenstrat, Fasta, FreqSum, VCF and other file formats used in population genetics analyses.
category: Bioinformatics
build-type: Simple
extra-source-files:
    README.md
    Changelog.md
    testDat/example.bim
    testDat/example.eigenstratgeno
    testDat/example.fasta
    testDat/example.freqsum
    testDat/example.histogram.txt
    testDat/example.ind
    testDat/example.snp
    testDat/example.vcf
    testDat/example.pileup

library
    build-depends: base <4.15

    exposed-modules:
        SequenceFormats.RareAlleleHistogram
        SequenceFormats.FreqSum
        SequenceFormats.Fasta
        SequenceFormats.VCF
        SequenceFormats.Eigenstrat
        SequenceFormats.Utils
        SequenceFormats.Pileup
    hs-source-dirs: src
    default-language: Haskell2010
    build-depends:
        base >=4.7 && <5,
        containers >=0.6.0.1,
        errors >=2.3.0,
        attoparsec >=0.13.2.2,
        pipes >=4.3.11,
        transformers >=0.5.6.2,
        bytestring >=0.10.8.2,
        lens-family >=1.2.3,
        pipes-bytestring >=2.1.6,
        foldl >=1.4.5,
        exceptions >=0.10.2,
        pipes-safe >=2.3.1,
        pipes-attoparsec >=0.5.1.5,
        vector >=0.12.0.3

test-suite sequenceFormatTests
    type: exitcode-stdio-1.0
    main-is: Spec.hs
    hs-source-dirs: test
    other-modules:
        SequenceFormats.EigenstratSpec
        SequenceFormats.FastaSpec
        SequenceFormats.FreqSumSpec
        SequenceFormats.RareAlleleHistogramSpec
        SequenceFormats.UtilsSpec
        SequenceFormats.VCFSpec
        SequenceFormats.PileupSpec
    default-language: Haskell2010
    build-depends:
        base >=4.12.0.0,
        sequence-formats -any,
        foldl >=1.4.5,
        pipes >=4.3.11,
        pipes-safe >=2.3.1,
        tasty >=1.2.3,
        vector >=0.12.0.3,
        transformers >=0.5.6.2,
        tasty-hunit >=0.10.0.2,
        bytestring >=0.10.8.2,
        containers >=0.6.0.1,
        hspec >=2.7.1