cobot-io 0.1.3.4 → 0.1.3.5

raw patch · 4 files changed

+11/−2 lines, 4 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

ChangeLog.md +4/−0
cobot-io.cabal +2/−2
src/Bio/ABI/Clean.hs +1/−0
test/ABISpec.hs +4/−0

ChangeLog.md view

@@ -2,6 +2,10 @@  ## [Unreleased] +## [0.1.3.5] - 2020-05-26+### Fixed+- Correctly clean `BasecalledSequenceWithRawData`, including inner quality.+ ## [0.1.3.4] - 2020-05-14 ### Added - `instance Cleanable BasecalledSequenceWithRawData`.

cobot-io.cabal view

@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: 05e68567b67639441d54b7151e50e0999a951e1a25a719e0ec4e701057148753+-- hash: b0510489dd9464931b8c53a26aa6930076e89ad4e6b1416041edb9cae7dd219b  name:           cobot-io-version:        0.1.3.4+version:        0.1.3.5 synopsis:       Biological data file formats and IO description:    Please see the README on GitHub at <https://github.com/biocad/cobot-io#readme> category:       Bio

src/Bio/ABI/Clean.hs view

@@ -80,6 +80,7 @@     let rightDroppedSequ = S.take (S.length leftDroppedSequ - toDropRight) leftDroppedSequ     let rightDroppedPloc = V.take (V.length leftDroppedPloc - toDropRight) leftDroppedPloc +    guard $ checkInner thr rightDroppedSequ     return input { bsSequence = rightDroppedSequ, bsPeakLocations = rightDroppedPloc }  -------------------------------------------------------------------------------

test/ABISpec.hs view

@@ -56,6 +56,10 @@     it "clean with raw data is the same as without" $ do       Right bsWithRaw <- decodeRawSequence <$> BSL.readFile "test/ABI/bad_at_the_end.ab1"       bsSequence <$> clean bsWithRaw `shouldBe` clean (bsSequence bsWithRaw)++    it "totally clean bad ABI file with raw data" $ do+      Right bsWithRaw <- decodeRawSequence <$> BSL.readFile "test/ABI/bad_quality.ab1"+      clean bsWithRaw `shouldBe` Nothing   where     checkFile :: FilePath -> Int -> Int -> String -> IO ()     checkFile path lengthBefore lengthAfter start = do