BiobaseXNA 0.9.2.0 → 0.9.2.1

raw patch · 5 files changed

+31/−15 lines, 5 filesdep ~PrimitiveArraydep ~aesondep ~file-embedPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependency ranges changed: PrimitiveArray, aeson, file-embed, lens, vector

API changes (from Hackage documentation)

Files

• Biobase/Primary/Letter.hs +3/−4
• Biobase/Secondary/Vienna.hs +3/−4
• BiobaseXNA.cabal +9/−6
• README.md +12/−1
• changelog.md +4/−0

@@ -12,8 +12,7 @@ import           Data.Ix (Ix(..)) import           Data.Serialize (Serialize(..)) import           Data.String (IsString(..))-import           Data.Vector.Fusion.Stream.Monadic (map,flatten,Step(..))-import           Data.Vector.Fusion.Stream.Size (Size (Unknown))+import           Data.Vector.Fusion.Stream.Monadic (map,Step(..)) import           Data.Vector.Unboxed.Deriving import           GHC.Base (remInt,quotInt) import           GHC.Generics (Generic)@@ -88,7 +87,7 @@   {-# Inline inBounds #-}  instance IndexStream z => IndexStream (z:.Letter l) where-  streamUp (ls:.Letter l) (hs:.Letter h) = flatten mk step Unknown $ streamUp ls hs+  streamUp (ls:.Letter l) (hs:.Letter h) = flatten mk step $ streamUp ls hs     where mk z = return (z,l)           step (z,k)             | k > h     = return $ Done@@ -96,7 +95,7 @@           {-# Inline [0] mk   #-}           {-# Inline [0] step #-}   {-# Inline streamUp #-}-  streamDown (ls:.Letter l) (hs:.Letter h) = flatten mk step Unknown $ streamDown ls hs+  streamDown (ls:.Letter l) (hs:.Letter h) = flatten mk step $ streamDown ls hs     where mk z = return (z,h)           step (z,k)             | k < l     = return $ Done

@@ -9,8 +9,7 @@ import           Data.Primitive.Types import           Data.Serialize (Serialize(..)) import           Data.Tuple (swap)-import           Data.Vector.Fusion.Stream.Monadic (map,flatten,Step(..))-import           Data.Vector.Fusion.Stream.Size (Size (Unknown))+import           Data.Vector.Fusion.Stream.Monadic (map,Step(..)) import           Data.Vector.Unboxed.Deriving import           GHC.Base (remInt,quotInt) import           GHC.Generics (Generic)@@ -51,7 +50,7 @@   {-# Inline inBounds #-}  instance IndexStream z => IndexStream (z:.ViennaPair) where-  streamUp (ls:.ViennaPair l) (hs:.ViennaPair h) = flatten mk step Unknown $ streamUp ls hs+  streamUp (ls:.ViennaPair l) (hs:.ViennaPair h) = flatten mk step $ streamUp ls hs     where mk z = return (z,l)           step (z,k)             | k > h     = return $ Done@@ -59,7 +58,7 @@           {-# Inline [0] mk   #-}           {-# Inline [0] step #-}   {-# Inline streamUp #-}-  streamDown (ls:.ViennaPair l) (hs:.ViennaPair h) = flatten mk step Unknown $ streamDown ls hs+  streamDown (ls:.ViennaPair l) (hs:.ViennaPair h) = flatten mk step $ streamDown ls hs     where mk z = return (z,h)           step (z,k)             | k < l     = return $ Done

@@ -1,5 +1,5 @@ name:           BiobaseXNA-version:        0.9.2.0+version:        0.9.2.1 author:         Christian Hoener zu Siederdissen maintainer:     choener@bioinf.uni-leipzig.de homepage:       https://github.com/choener/BiobaseXNA@@ -41,11 +41,14 @@   changelog.md   README.md +data-files:+  sources/iupac-nucleotides  + library   build-depends: base                     >= 4.7      && < 4.9-               , aeson                    >= 0.8      && < 0.10+               , aeson                    >= 0.8      && < 0.11                , bimaps                   >= 0.0.0.2  && < 0.0.1.0                , binary                   >= 0.7      && < 0.8                , bytes                    >= 0.15     && < 0.16@@ -55,15 +58,15 @@                , containers               >= 0.5      && < 0.6                , csv                      >= 0.1      && < 0.2                , deepseq                  >= 1.3      && < 1.5-               , file-embed               >= 0.0.8    && < 0.0.9+               , file-embed               >= 0.0.8    && < 0.0.10                , hashable                 >= 1.2      && < 1.3-               , lens                     >= 4.0      && < 4.13+               , lens                     >= 4.0      && < 4.14                , primitive                >= 0.5      && < 0.7-               , PrimitiveArray           >= 0.6.0    && < 0.6.2+               , PrimitiveArray           >= 0.7.0    && < 0.7.1                , split                    >= 0.2      && < 0.3                , text                     >= 1.0      && < 1.3                , tuple                    >= 0.3      && < 0.4-               , vector                   >= 0.10     && < 0.11+               , vector                   >= 0.10     && < 0.12                , vector-binary-instances  >= 0.2      && < 0.3                , vector-th-unbox          >= 0.2      && < 0.3   exposed-modules:

@@ -2,7 +2,18 @@  # BiobaseXNA -Efficient encoding of biological sequences.+Efficient encoding of (short) biological sequences. This package ist designed+to deal with *in-memory* snippets of DNA, RNA, and amino acids. The encoding is+geared toward time-efficiency, not necessarily space efficiency (we use Int's+for encoding characters, not the smallest type possible).++Additional modules provide conversion capabilities between different types of+characters according to biological laws, and some biochemical constraint+information. The latter includes canonical and non-canonical pairing+information for RNA.++Actual energy parameters for pairings are provided by other packages, for+example BiobaseTurner for the loop energy model with measured parameters.   

@@ -1,3 +1,7 @@+0.9.2.1++- stack.yaml, some version bumping+ 0.9.2.0 -------