version 0.1.3.5: fix clean sequence with raw data (#39)

ChangeLog.md

@@ -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`.

package.yaml

@@ -1,5 +1,5 @@
 name:                cobot-io
-version:             0.1.3.4
+version:             0.1.3.5
 github:              "biocad/cobot-io"
 license:             BSD3
 category:            Bio

src/Bio/ABI/Clean.hs

@@ -80,6 +80,7 @@ instance Cleanable BasecalledSequenceWithRawData where
     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

@@ -56,6 +56,10 @@ abiCleanSpec =
     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