diversity 0.6.0.0 → 0.6.0.1

raw patch · 2 files changed

+3/−26 lines, 2 filesdep ~fastaPVP ok

version bump matches the API change (PVP)

Dependency ranges changed: fasta

API changes (from Hackage documentation)

Files

• diversity.cabal +3/−3
• src/src-exec/Main.hs +0/−23

@@ -2,7 +2,7 @@ -- documentation, see http://haskell.org/cabal/users-guide/  name:                diversity-version:             0.6.0.0+version:             0.6.0.1 synopsis:            Return the diversity at each position for all sequences in a fasta file description:         Find the diversity of a collection of entities, mainly for use with fasta sequences. Produces a binary which works on fasta files to find the diversity of any order and rarefaction curves for a sliding window across all positions in the sequences. To analyze just a collection of entities, just use the whole sequences and list flag. homepage:            https://github.com/GregorySchwartz/diversity@@ -20,7 +20,7 @@   hs-source-dirs:      src/src-lib   exposed-modules:     Math.Diversity.Types, Math.Diversity.Diversity, Math.Diversity.GenerateDiversity, Math.Diversity.Print, Math.Diversity.Statistics, Math.Diversity.RandomSampling   -- other-modules:-  build-depends:       base >=4.6 && <4.9, containers >=0.5 && <0.6, split >=0.2 && <0.3, parsec >=3.1 && <4.0, fasta >=0.5.3 && <0.6, math-functions >=0.1 && <0.2, scientific >= 0.3 && < 0.4, random-shuffle >=0.0 && < 0.1, MonadRandom >=0.3 && <0.4+  build-depends:       base >=4.6 && <4.9, containers >=0.5 && <0.6, split >=0.2 && <0.3, parsec >=3.1 && <4.0, fasta >=0.5.4 && <0.6, math-functions >=0.1 && <0.2, scientific >= 0.3 && < 0.4, random-shuffle >=0.0 && < 0.1, MonadRandom >=0.3 && <0.4  executable diversity   ghc-options: -O2@@ -28,4 +28,4 @@   hs-source-dirs:      src/src-exec   main-is:             Main.hs   -- other-modules:       -  build-depends:       diversity, base >=4.6 && <4.9, optparse-applicative >=0.10 && <0.12, fasta >=0.5.3 && <0.6, pipes >= 4.1 && < 4.2, containers >=0.5 && <0.6+  build-depends:       diversity, base >=4.6 && <4.9, optparse-applicative >=0.10 && <0.12, fasta >=0.5.4 && <0.6, pipes >= 4.1 && < 4.2, containers >=0.5 && <0.6

@@ -159,29 +159,6 @@          <> help "The csv file containing the diversities at each position.\                  \ expects a string, so you need a string wven with std" ) -pipesFasta :: (MonadIO m) => IO.Handle -> Pipe String FastaSequence m ()-pipesFasta h = do-    first <- await-    getRest first ""-  where-    getRest x !acc = do-        eof <- liftIO $ IO.hIsEOF h-        if eof-            then yield FastaSequence { fastaHeader = tail x-                                     , fastaSeq    = filter-                                                     (`notElem` "\n\r ")-                                                     acc }-            else do-                y <- await-                if take 1 y == ">"-                    then do-                        yield FastaSequence { fastaHeader = tail x-                                            , fastaSeq    = filter-                                                            (`notElem` "\n\r ")-                                                            acc }-                        getRest y ""-                    else getRest x (acc ++ y)- pipesPositionMap :: Options -> IO PositionMap pipesPositionMap opts = do     h <- if null . inputFasta $ opts