MutationOrder-0.0.1.0: MutationOrder.cabal
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