cabal-version: >=1.10
name: sequence-formats
version: 1.8.0.0
license: GPL-3
license-file: LICENSE
maintainer: stephan.schiffels@mac.com
author: Stephan Schiffels
homepage: https://github.com/stschiff/sequence-formats
bug-reports: https://github.com/stschiff/sequence-formats/issues
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.
category: Bioinformatics
build-type: Simple
extra-source-files:
README.md
Changelog.md
testDat/example.bim
testDat/example.bed
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
exposed-modules:
SequenceFormats.RareAlleleHistogram
SequenceFormats.FreqSum
SequenceFormats.Fasta
SequenceFormats.VCF
SequenceFormats.Eigenstrat
SequenceFormats.Plink
SequenceFormats.Utils
SequenceFormats.Pileup
SequenceFormats.Bed
SequenceFormats.Genomic
hs-source-dirs: src
default-language: Haskell2010
build-depends:
base >=4.7 && <5,
containers,
errors,
attoparsec,
pipes,
transformers,
bytestring,
lens-family,
pipes-bytestring,
foldl,
exceptions,
pipes-safe,
pipes-attoparsec,
vector
test-suite sequenceFormatTests
type: exitcode-stdio-1.0
main-is: Spec.hs
hs-source-dirs: test
other-modules:
SequenceFormats.EigenstratSpec
SequenceFormats.BedSpec
SequenceFormats.FastaSpec
SequenceFormats.FreqSumSpec
SequenceFormats.RareAlleleHistogramSpec
SequenceFormats.UtilsSpec
SequenceFormats.PlinkSpec
SequenceFormats.VCFSpec
SequenceFormats.PileupSpec
default-language: Haskell2010
build-depends:
base,
sequence-formats,
foldl,
pipes,
pipes-safe,
tasty,
vector,
transformers,
tasty-hunit,
bytestring,
containers,
hspec