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BiobaseBlast 0.3.0.0 → 0.3.1.0

raw patch · 4 files changed

+16/−5 lines, 4 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

- Biobase.BLAST.Types: HitDescription :: !Text -> !Text -> !Text -> !Int -> HitDescription
+ Biobase.BLAST.Types: HitDescription :: !Text -> !Text -> !Text -> Maybe Int -> HitDescription
- Biobase.BLAST.Types: [$sel:_taxid:HitDescription] :: HitDescription -> !Int
+ Biobase.BLAST.Types: [$sel:_taxid:HitDescription] :: HitDescription -> Maybe Int
- Biobase.BLAST.Types: taxid :: Lens' HitDescription Int
+ Biobase.BLAST.Types: taxid :: Lens' HitDescription (Maybe Int)
- Biobase.SubstMatrix.Types: aaSubstMat :: forall t_aQ9N s_aQ9O a_aQ9P t_aS28 s_aS29 a_aS2a. Iso (AASubstMat t_aQ9N s_aQ9O a_aQ9P) (AASubstMat t_aS28 s_aS29 a_aS2a) (Unboxed ((:.) ((:.) Z (Letter AA a_aQ9P)) (Letter AA a_aQ9P)) s_aQ9O) (Unboxed ((:.) ((:.) Z (Letter AA a_aS2a)) (Letter AA a_aS2a)) s_aS29)
+ Biobase.SubstMatrix.Types: aaSubstMat :: forall t_aQo8 s_aQo9 a_aQoa t_aSgr s_aSgs a_aSgt. Iso (AASubstMat t_aQo8 s_aQo9 a_aQoa) (AASubstMat t_aSgr s_aSgs a_aSgt) (Unboxed ((:.) ((:.) Z (Letter AA a_aQoa)) (Letter AA a_aQoa)) s_aQo9) (Unboxed ((:.) ((:.) Z (Letter AA a_aSgt)) (Letter AA a_aSgt)) s_aSgs)
- Biobase.SubstMatrix.Types: anuc1SubstMat :: forall t_aSuP s_aSuQ a_aSuR n_aSuS t_aSHZ s_aSI0 a_aSI1 n_aSI2. Iso (ANuc1SubstMat t_aSuP s_aSuQ a_aSuR n_aSuS) (ANuc1SubstMat t_aSHZ s_aSI0 a_aSI1 n_aSI2) (Unboxed ((:.) ((:.) Z (Letter AA a_aSuR)) (Letter DNA n_aSuS)) s_aSuQ) (Unboxed ((:.) ((:.) Z (Letter AA a_aSI1)) (Letter DNA n_aSI2)) s_aSI0)
+ Biobase.SubstMatrix.Types: anuc1SubstMat :: forall t_aSJ8 s_aSJ9 a_aSJa n_aSJb t_aSWi s_aSWj a_aSWk n_aSWl. Iso (ANuc1SubstMat t_aSJ8 s_aSJ9 a_aSJa n_aSJb) (ANuc1SubstMat t_aSWi s_aSWj a_aSWk n_aSWl) (Unboxed ((:.) ((:.) Z (Letter AA a_aSJa)) (Letter DNA n_aSJb)) s_aSJ9) (Unboxed ((:.) ((:.) Z (Letter AA a_aSWk)) (Letter DNA n_aSWl)) s_aSWj)
- Biobase.SubstMatrix.Types: anuc2SubstMat :: forall t_aSh0 s_aSh1 a_aSh2 n_aSh3 t_aSuG s_aSuH a_aSuI n_aSuJ. Iso (ANuc2SubstMat t_aSh0 s_aSh1 a_aSh2 n_aSh3) (ANuc2SubstMat t_aSuG s_aSuH a_aSuI n_aSuJ) (Unboxed ((:.) ((:.) ((:.) Z (Letter AA a_aSh2)) (Letter DNA n_aSh3)) (Letter DNA n_aSh3)) s_aSh1) (Unboxed ((:.) ((:.) ((:.) Z (Letter AA a_aSuI)) (Letter DNA n_aSuJ)) (Letter DNA n_aSuJ)) s_aSuH)
+ Biobase.SubstMatrix.Types: anuc2SubstMat :: forall t_aSvj s_aSvk a_aSvl n_aSvm t_aSIZ s_aSJ0 a_aSJ1 n_aSJ2. Iso (ANuc2SubstMat t_aSvj s_aSvk a_aSvl n_aSvm) (ANuc2SubstMat t_aSIZ s_aSJ0 a_aSJ1 n_aSJ2) (Unboxed ((:.) ((:.) ((:.) Z (Letter AA a_aSvl)) (Letter DNA n_aSvm)) (Letter DNA n_aSvm)) s_aSvk) (Unboxed ((:.) ((:.) ((:.) Z (Letter AA a_aSJ1)) (Letter DNA n_aSJ2)) (Letter DNA n_aSJ2)) s_aSJ0)
- Biobase.SubstMatrix.Types: anuc3SubstMat :: forall t_aS2i s_aS2j a_aS2k n_aS2l t_aSgR s_aSgS a_aSgT n_aSgU. Iso (ANuc3SubstMat t_aS2i s_aS2j a_aS2k n_aS2l) (ANuc3SubstMat t_aSgR s_aSgS a_aSgT n_aSgU) (Unboxed ((:.) ((:.) ((:.) ((:.) Z (Letter AA a_aS2k)) (Letter DNA n_aS2l)) (Letter DNA n_aS2l)) (Letter DNA n_aS2l)) s_aS2j) (Unboxed ((:.) ((:.) ((:.) ((:.) Z (Letter AA a_aSgT)) (Letter DNA n_aSgU)) (Letter DNA n_aSgU)) (Letter DNA n_aSgU)) s_aSgS)
+ Biobase.SubstMatrix.Types: anuc3SubstMat :: forall t_aSgB s_aSgC a_aSgD n_aSgE t_aSva s_aSvb a_aSvc n_aSvd. Iso (ANuc3SubstMat t_aSgB s_aSgC a_aSgD n_aSgE) (ANuc3SubstMat t_aSva s_aSvb a_aSvc n_aSvd) (Unboxed ((:.) ((:.) ((:.) ((:.) Z (Letter AA a_aSgD)) (Letter DNA n_aSgE)) (Letter DNA n_aSgE)) (Letter DNA n_aSgE)) s_aSgC) (Unboxed ((:.) ((:.) ((:.) ((:.) Z (Letter AA a_aSvc)) (Letter DNA n_aSvd)) (Letter DNA n_aSvd)) (Letter DNA n_aSvd)) s_aSvb)

Files

Biobase/BLAST/Import.hs view
@@ -24,7 +24,7 @@ import Debug.Trace import Text.Printf import Biobase.BLAST.Types-import Data.Aeson as A+import qualified Data.Aeson as A  -- | reads and parses tabular Blast result from provided filePath blastCmdJSON2FromFile :: String -> IO (Either String BlastCmdJSON2)
Biobase/BLAST/Types.hs view
@@ -156,7 +156,7 @@     _id :: !T.Text,     _accession :: !T.Text,     _title :: !T.Text,-    _taxid :: !Int+    _taxid :: Maybe Int     --_sciname :: !T.Text   }   deriving (Show, Eq, Generic)
BiobaseBlast.cabal view
@@ -1,5 +1,5 @@ name:           BiobaseBlast-version:        0.3.0.0+version:        0.3.1.0 author:         Christian Hoener zu Siederdissen, Florian Eggenhofer maintainer:     choener@bioinf.uni-leipzig.de homepage:       https://github.com/choener/BiobaseBlast@@ -221,5 +221,5 @@  source-repository this   type:     git-  location: https://github.com/choener/BiobaseBlast/tree/0.3.0.0-  tag:      0.3.0.0+  location: https://github.com/choener/BiobaseBlast/tree/0.3.1.0+  tag:      0.3.1.0
changelog.md view
@@ -1,3 +1,14 @@+0.3.1.0+-------++- Blast datatype supports optional taxonomy id++0.3.0.1+-------++- Fix for newly ambigous ? operator export from attoparsec and aeson>=1.4.4.0 +  in Import module + 0.3.0.0 -------