cabal-version: >=1.10
name: sequence-formats
version: 1.4.1
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
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