hyraxAbif 0.2.3.15 → 0.2.3.21
raw patch · 3 files changed
+35/−16 lines, 3 filesdep ~binarydep ~bytestringdep ~directoryPVP ok
version bump matches the API change (PVP)
Dependency ranges changed: binary, bytestring, directory, protolude, text
API changes (from Hackage documentation)
Files
- LICENSE +2/−2
- app/Main.hs +20/−1
- hyraxAbif.cabal +13/−13
LICENSE view
@@ -3,7 +3,7 @@ -------------------------------------------------------------------------------- BSD-3-Clause ---------------------------------------------------------------------------------Copyright HyraxBio (c) 2018/2019+Copyright HyraxBio (c) 2018-2020 All rights reserved. @@ -40,7 +40,7 @@ Apache 2.0 -------------------------------------------------------------------------------- -Copyright HyraxBio (c) 2018/2019+Copyright HyraxBio (c) 2018-2020 Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
app/Main.hs view
@@ -14,6 +14,7 @@ import qualified Hyrax.Abif as H import qualified Hyrax.Abif.Read as H+import qualified Hyrax.Abif.Write as H import qualified Hyrax.Abif.Generate as H main :: IO ()@@ -23,7 +24,8 @@ case headMay args of Just "dump" -> runDump Just "gen" -> runGenerateAb1- _ -> putText "unknown args, expecting dump/gen"+ Just "strip" -> runStrip+ _ -> putText "unknown args, expecting dump/gen/strip" runGenerateAb1 :: IO ()@@ -59,6 +61,23 @@ ) <$> debugged _ -> putText "Expecting path to ab1"+++runStrip :: IO ()+runStrip =+ Env.getArgs >>= \case+ [_, source, dest] ->+ H.readAbif source >>= \case+ Right orig -> do+ let filterDir d = H.dTagName d `elem` ["DATA","FWO_","LANE","PBAS","PDMF","PLOC","S/N%","SMPL"]+ let stripped' = orig { H.aDirs = filter filterDir (H.aDirs orig) }+ let stripped = H.addDirectory stripped' $ H.mkComment "Stripped by HyraxABIF"+ H.writeAbif dest stripped++ Left e -> putText $ "Error reading source\n" <> e++ _ ->+ putText "Expecting source and dest path" myColourPrefs :: Clr.ColourPrefs
hyraxAbif.cabal view
@@ -1,13 +1,13 @@ cabal-version: 2.2 name: hyraxAbif-version: 0.2.3.15+version: 0.2.3.21 synopsis: Modules for parsing, generating and manipulating AB1 files. homepage: https://github.com/hyraxbio/hyraxAbif/#readme license: BSD-3-Clause OR Apache-2.0 license-file: LICENSE author: HyraxBio-maintainer: andre@hyraxbio.co.za, andre@andrevdm.com-copyright: 2018 HyraxBio+maintainer: andre@hyraxbio.co.za+copyright: 2018-2020 HyraxBio category: Bioinformatics build-type: Simple extra-source-files: README.md@@ -44,10 +44,10 @@ , Examples.ReadAb1 build-depends: base >= 4.9.1.0 && < 5 , protolude >= 0.2.2 && < 0.2.5- , text >= 1.2.3.0 && < 1.2.4.0- , bytestring >= 0.10.8.2 && < 0.10.9.0- , binary >= 0.8.5.1 && < 0.8.7.0- , directory >= 1.3.0.2 && < 1.3.4.0+ , text >= 1.2.3.0 && < 1.2.5.0+ , bytestring >= 0.10.8.2 && < 0.10.11.0+ , binary >= 0.8.5.1 && < 0.8.8.0+ , directory >= 1.3.0.2 && < 1.3.5.0 , filepath >= 1.4.1.2 && < 1.4.3.0 default-language: Haskell2010 @@ -58,8 +58,8 @@ build-depends: base >= 4.9.1.0 && < 5 , hyraxAbif , protolude >= 0.2.2 && < 0.2.5- , text >= 1.2.3.0 && < 1.2.4.0- , bytestring >= 0.10.8.2 && < 0.10.9.0+ , text >= 1.2.3.0 && < 1.2.5.0+ , bytestring >= 0.10.8.2 && < 0.10.11.0 , pretty-show >= 1.6.16 && < 1.10.0 , hscolour >= 1.24.4 && < 1.25.0 default-language: Haskell2010@@ -71,10 +71,10 @@ build-depends: base >= 4.9.1.0 && < 5 , hyraxAbif , protolude >= 0.2.2 && < 0.2.5- , text >= 1.2.3.0 && < 1.2.4.0- , bytestring >= 0.10.8.2 && < 0.10.9.0- , binary >= 0.8.5.1 && < 0.8.7.0- , hedgehog >= 0.5.3 && < 0.6.2+ , text >= 1.2.3.0 && < 1.2.5.0+ , bytestring >= 0.10.8.2 && < 0.10.11.0+ , binary >= 0.8.5.1 && < 0.8.8.0+ , hedgehog >= 0.5.3 && < 1.1.0 other-modules: AbifTests , FastaTests , Generators