diff --git a/sequence-formats.cabal b/sequence-formats.cabal --- a/sequence-formats.cabal +++ b/sequence-formats.cabal @@ -1,64 +1,100 @@ -name: sequence-formats -version: 1.8.1.0 -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 +cabal-version: >=1.10 +name: sequence-formats +version: 1.8.1.1 +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. -extra-source-files: README.md, - Changelog.md, - 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 +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.bed + testDat/example.eigenstratgeno + testDat/example.eigenstratgeno.gz + testDat/example.fam + testDat/example.fasta + testDat/example.freqsum + testDat/example.histogram.txt + testDat/example.ind + testDat/example.pileup + testDat/example.plink.bed + testDat/example.plink.bed.gz + testDat/example.plink.bim + testDat/example.plink.bim.gz + testDat/example.plink.fam + testDat/example.snp + testDat/example.snp.gz + testDat/example.vcf + testDat/example.vcf.gz + 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 - build-depends: base >= 4.7 && < 5, containers, errors, attoparsec, pipes, - transformers, bytestring, lens-family, - pipes-bytestring, foldl, exceptions, pipes-safe, - pipes-attoparsec, vector, pipes-zlib - default-language: Haskell2010 + exposed-modules: + SequenceFormats.RareAlleleHistogram + SequenceFormats.FreqSum + SequenceFormats.Fasta + SequenceFormats.VCF + SequenceFormats.Eigenstrat + SequenceFormats.Plink + SequenceFormats.Utils + SequenceFormats.Pileup + SequenceFormats.Bed + SequenceFormats.Genomic -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.BedSpec, - SequenceFormats.FastaSpec, - SequenceFormats.FreqSumSpec, - SequenceFormats.RareAlleleHistogramSpec, - SequenceFormats.UtilsSpec, - SequenceFormats.PlinkSpec, - SequenceFormats.VCFSpec, - SequenceFormats.PileupSpec - default-language: Haskell2010 + hs-source-dirs: src + default-language: Haskell2010 + build-depends: + base >=4.7 && <5, + containers >=0.6.7, + errors >=2.3.0, + attoparsec >=0.14.4, + pipes >=4.3.16, + transformers >=0.5.6.2, + bytestring >=0.11.5.2, + lens-family >=2.1.2, + pipes-bytestring >=2.1.7, + foldl >=1.4.15, + exceptions >=0.10.5, + pipes-safe >=2.3.4, + pipes-attoparsec >=0.6.0, + vector >=0.13.1.0, + pipes-zlib >=0.4.4.2 + +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 >=4.17.2.0, + sequence-formats, + foldl >=1.4.15, + pipes >=4.3.16, + pipes-safe >=2.3.4, + tasty >=1.4.3, + vector >=0.13.1.0, + transformers >=0.5.6.2, + tasty-hunit >=0.10.1, + bytestring >=0.11.5.2, + containers >=0.6.7, + hspec >=2.10.10 diff --git a/testDat/example.eigenstratgeno.gz b/testDat/example.eigenstratgeno.gz new file mode 100644 Binary files /dev/null and b/testDat/example.eigenstratgeno.gz differ diff --git a/testDat/example.plink.bed.gz b/testDat/example.plink.bed.gz new file mode 100644 Binary files /dev/null and b/testDat/example.plink.bed.gz differ diff --git a/testDat/example.plink.bim.gz b/testDat/example.plink.bim.gz new file mode 100644 Binary files /dev/null and b/testDat/example.plink.bim.gz differ diff --git a/testDat/example.snp.gz b/testDat/example.snp.gz new file mode 100644 Binary files /dev/null and b/testDat/example.snp.gz differ diff --git a/testDat/example.vcf.gz b/testDat/example.vcf.gz new file mode 100644 Binary files /dev/null and b/testDat/example.vcf.gz differ