name:                sequence-formats
version:             1.5.1.3
x-revision: 1
synopsis:            A package with basic parsing utilities for several Bioinformatic data formats.
description:         Contains utilities to parse and write Eigenstrat, Fasta, FreqSum, VCF, Plink and other file formats used in population genetics analyses.
license:             GPL-3
license-file:        LICENSE
author:              Stephan Schiffels
maintainer:          stephan.schiffels@mac.com
category:            Bioinformatics
build-type:          Simple
cabal-version:       >=1.10
Homepage:	           https://github.com/stschiff/sequence-formats
Bug-Reports:         https://github.com/stschiff/sequence-formats/issues

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
                     testDat/example.fam
                     testDat/example.plink.bed
                     testDat/example.plink.fam
                     testDat/example.plink.bim

library
  build-depends: base <4.15

  exposed-modules:     SequenceFormats.RareAlleleHistogram,
                       SequenceFormats.FreqSum,
                       SequenceFormats.Fasta,
                       SequenceFormats.VCF,
                       SequenceFormats.Eigenstrat,
                       SequenceFormats.Plink,
                       SequenceFormats.Utils,
                       SequenceFormats.Pileup
  hs-source-dirs:      src
  build-depends:       base >= 4.7 && < 5, containers, errors, attoparsec, pipes,
                       transformers, bytestring, lens-family,
                       pipes-bytestring, foldl, exceptions, pipes-safe,
                       pipes-attoparsec, vector
  default-language:    Haskell2010

Test-Suite sequenceFormatTests
  type:                exitcode-stdio-1.0
  main-is:             Spec.hs
  hs-source-dirs:      test
  build-depends:       base, sequence-formats, foldl, pipes, pipes-safe, tasty, vector,
                       transformers, tasty-hunit, bytestring, containers, hspec
  other-modules:       SequenceFormats.EigenstratSpec,
                       SequenceFormats.FastaSpec,
                       SequenceFormats.FreqSumSpec,
                       SequenceFormats.RareAlleleHistogramSpec,
                       SequenceFormats.UtilsSpec,
                       SequenceFormats.PlinkSpec,
                       SequenceFormats.VCFSpec,
                       SequenceFormats.PileupSpec
  default-language:    Haskell2010