bio 0.4.5 → 0.4.6

raw patch · 3 files changed

+2/−17 lines, 3 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• Bio/Alignment/AlignData.hs +0/−2
• Bio/Sequence.hs +1/−14
• bio.cabal +1/−1

@@ -41,8 +41,6 @@  -- | Gaps are coded as '*'s, this function removes them, and returns --   the sequence along with the list of gap positions.---   note that gaps are positioned relative to the *gapped* sequence ---   (contrast to stmassembler/Cluster.hs) extractGaps :: SeqData -> (SeqData,Gaps) extractGaps str = (BC.filter (/='*') str,BC.elemIndices '*' str) 

@@ -21,10 +21,7 @@     -- ** Other utility functions     , defragSeq, seqmap -    -- * File IO-    -- ** Generic sequence reading-    , readNuc, readProt-+    -- * File formats     -- ** The Fasta file format ("Bio.Sequence.Fasta")     , readFasta, hReadFasta      , writeFasta, hWriteFasta@@ -70,13 +67,3 @@ -- sequence-oriented stuff import Bio.Sequence.Entropy import Bio.Sequence.HashWord---- | Read nucleotide sequences in any format - Fasta, SFF, FastQ, 2bit, PHD...-readNuc :: FilePath -> IO [Sequence Nuc]-readNuc = undefined-          -- check file contents-          -- magic number---- | Read protein sequences in any supported format (i.e. Fasta)-readProt :: FilePath -> IO [Sequence Amino]-readProt xs = map castSeq `fmap` readFasta xs

@@ -1,5 +1,5 @@ Name:                bio-Version:             0.4.5+Version:             0.4.6 License:             LGPL License-file:        LICENSE Author:              Ketil Malde