name: MutationOrder version: 0.0.1.0 author: Maria Beatriz Walter Costa, Christian Hoener zu Siederdissen, 2017 copyright: Maria Beatriz Walter Costa, Christian Hoener zu Siederdissen, 2017 homepage: https://github.com/choener/MutationOrder bug-reports: https://github.com/choener/MutationOrder/issues maintainer: choener@bioinf.uni-leipzig.de category: Bioinformatics license: GPL-3 license-file: LICENSE build-type: Simple stability: experimental cabal-version: >= 1.10.0 tested-with: GHC == 8.0.2 synopsis: Most likely order of mutation events in RNA description: Determine the most likely order in which single nucleotide mutations happened between two RNA sequences. . Developed to analyse the @HAR 1@ region, but agnostic to the actual sequences and can be used to analyze any RNA sequence that fits the algorithmic constraints. . As long as the two input RNAs are small enough enough (couple hundred nucleotides) and the number of mutations is small enough (around 20-26, since the algorithm is exponential in this number) the algorithm should work for similar problems without changes. . We currently only consider point mutations, not in-dels. Extra-Source-Files: README.md changelog.md flag debug description: Enable bounds checking and various other debug operations at the cost of a significant performance penalty. default: False manual: True flag debugoutput description: Enable debug output, which spams the screen full of index information default: False manual: True library build-depends: base >= 4.7 && < 5.0 , aeson >= 1.1 , attoparsec >= 0.13 , bytestring , bytestring-trie >= 0.2 , cereal >= 0.5 , cereal-vector >= 0.2 , containers , deepseq >= 1.4 , directory , errors >= 2.0 , filemanip >= 0.3 , filepath , hashable >= 1.2 , lens >= 4.0 , log-domain >= 0.10 , mtl , parallel >= 3.2 , serialize-instances >= 0.1 , split >= 0.2 , text >= 1.0 , unordered-containers >= 0.2.7 , vector >= 0.11 , vector-strategies >= 0.4 , zlib >= 0.6 -- , ADPfusion == 0.5.2.* , ADPfusionSet == 0.0.0.* , bimaps == 0.1.0.* , BiobaseXNA == 0.9.3.* , DPutils == 0.0.1.* , FormalGrammars == 0.3.1.* , OrderedBits == 0.0.1.* , PrimitiveArray == 0.8.0.* , PrimitiveArray-Pretty == 0.0.0.* , ShortestPathProblems == 0.0.0.* , ViennaRNA-bindings == 0.233.1.* exposed-modules: BioInf.MutationOrder BioInf.MutationOrder.EdgeProb BioInf.MutationOrder.MinDist BioInf.MutationOrder.RNA BioInf.MutationOrder.SequenceDB BioInf.MutationOrder.BackMutations default-extensions: BangPatterns , CPP , DeriveDataTypeable , DeriveGeneric , FlexibleContexts , GADTs , LambdaCase , MultiParamTypeClasses , MultiWayIf , OverloadedStrings , QuasiQuotes , RecordWildCards , ScopedTypeVariables , TemplateHaskell , TupleSections , TypeFamilies , TypeOperators , UnicodeSyntax default-language: Haskell2010 ghc-options: -O2 -funbox-strict-fields if flag(debug) cpp-options: -DADPFUSION_CHECKS ghc-options: -fno-ignore-asserts -O0 if flag(debugoutput) cpp-options: -DADPFUSION_DEBUGOUTPUT executable MutationOrder build-depends: base , bytestring , cmdargs >= 0.10 , directory , errors , file-embed >= 0.0.8 , filepath -- , MutationOrder hs-source-dirs: src default-extensions: BangPatterns , DeriveDataTypeable , RecordWildCards , TemplateHaskell , UnicodeSyntax default-language: main-is: MutationOrder.hs default-language: Haskell2010 ghc-options: -O2 -rtsopts -- -threaded test-suite properties type: exitcode-stdio-1.0 main-is: properties.hs ghc-options: -threaded -rtsopts -with-rtsopts=-N hs-source-dirs: tests default-language: Haskell2010 default-extensions: BangPatterns , CPP , FlexibleContexts , FlexibleInstances , MultiParamTypeClasses , ScopedTypeVariables , TemplateHaskell , TypeFamilies , TypeOperators , TypeSynonymInstances build-depends: base , QuickCheck , tasty >= 0.11 , tasty-quickcheck >= 0.8 , tasty-th >= 0.1 , vector -- , MutationOrder source-repository head type: git location: git://github.com/choener/MutationOrder source-repository this type: git location: git://github.com/choener/MutationOrder/tree/0.0.1.0 tag: 0.0.1.0