diff --git a/sequence-formats.cabal b/sequence-formats.cabal --- a/sequence-formats.cabal +++ b/sequence-formats.cabal @@ -1,61 +1,91 @@ -name: sequence-formats -version: 1.5.1.4 -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: 1.5.2 +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.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 +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.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 - 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 + exposed-modules: + SequenceFormats.RareAlleleHistogram + SequenceFormats.FreqSum + SequenceFormats.Fasta + SequenceFormats.VCF + SequenceFormats.Eigenstrat + SequenceFormats.Plink + SequenceFormats.Utils + SequenceFormats.Pileup -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 + 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.PlinkSpec + 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 diff --git a/src/SequenceFormats/Eigenstrat.hs b/src/SequenceFormats/Eigenstrat.hs --- a/src/SequenceFormats/Eigenstrat.hs +++ b/src/SequenceFormats/Eigenstrat.hs @@ -71,8 +71,8 @@ chrom <- A.skipMany1 A.space >> word geneticPos <- A.skipMany1 A.space >> A.double pos <- A.skipMany1 A.space >> A.decimal - ref <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGN") - alt <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGX") + ref <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGNX") + alt <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGNX") void A.endOfLine return $ EigenstratSnpEntry (Chrom chrom) pos geneticPos snpId_ ref alt diff --git a/src/SequenceFormats/Plink.hs b/src/SequenceFormats/Plink.hs --- a/src/SequenceFormats/Plink.hs +++ b/src/SequenceFormats/Plink.hs @@ -36,8 +36,8 @@ snpId_ <- A.skipMany1 A.space >> word geneticPos <- A.skipMany1 A.space >> A.double pos <- A.skipMany1 A.space >> A.decimal - ref <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGN01234") - alt <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGX01234") + ref <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGNX01234") + alt <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGNX01234") void A.endOfLine let refConvert = convertNum ref altConvert = convertNum alt