modify-fasta 0.8.0.1 → 0.8.0.2
raw patch · 2 files changed
+6/−6 lines, 2 files
Files
- modify-fasta.cabal +1/−1
- src/Main.hs +5/−5
modify-fasta.cabal view
@@ -2,7 +2,7 @@ -- documentation, see http://haskell.org/cabal/users-guide/ name: modify-fasta-version: 0.8.0.1+version: 0.8.0.2 synopsis: Modify fasta (and CLIP) files in several optional ways -- description: homepage: https://github.com/GregorySchwartz/modify-fasta
src/Main.hs view
@@ -35,7 +35,7 @@ -- Command line arguments data Options = Options { input :: String- , aminoAcidsFlag :: String+ , aminoAcidsFlag :: GeneticUnit , legacyFlag :: Bool , clipFastaFlag :: Bool , convertToAminoAcidsFlag :: Bool@@ -78,10 +78,10 @@ <> metavar "FILE" <> value "" <> help "The input fasta file or CLIP fasta file" )- <*> strOption+ <*> option auto ( long "unit" <> short 'u'- <> metavar "AminoAcid|Nucleotide"+ <> metavar "AminoAcid | Nucleotide" <> help "Whether these sequences are composed of\ \ amino acids (AminoAcid) or nucleotides (Nucleotide)" ) <*> switch@@ -321,7 +321,7 @@ hOut <- if null . output $ opts then return IO.stdout else IO.openFile (output opts) IO.WriteMode- let genUnit = read . aminoAcidsFlag $ opts+ let genUnit = aminoAcidsFlag opts stopRange = inputStopRange opts customFilters = fieldIntParser . inputCustomFilter $ opts changeFields = fieldIntParser . inputChangeField $ opts@@ -484,7 +484,7 @@ then T.getContents else T.readFile . input $ opts -- No redundant newlines in sequence- let genUnit = read . aminoAcidsFlag $ opts+ let genUnit = aminoAcidsFlag opts stopRange = inputStopRange opts codonMut = inputCodonMut opts codonMutType = T.pack . inputCodonMutType $ opts