sequence-formats 1.5.1.4 → 1.5.2
raw patch · 3 files changed
+91/−61 lines, 3 filesdep ~attoparsecdep ~basedep ~bytestringPVP ok
version bump matches the API change (PVP)
Dependency ranges changed: attoparsec, base, bytestring, containers, errors, exceptions, foldl, hspec, lens-family, pipes, pipes-attoparsec, pipes-bytestring, pipes-safe, tasty, tasty-hunit, transformers, vector
API changes (from Hackage documentation)
Files
- sequence-formats.cabal +87/−57
- src/SequenceFormats/Eigenstrat.hs +2/−2
- src/SequenceFormats/Plink.hs +2/−2
sequence-formats.cabal view
@@ -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
src/SequenceFormats/Eigenstrat.hs view
@@ -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
src/SequenceFormats/Plink.hs view
@@ -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