bioinformatics-toolkit 0.9.1 → 0.9.2
raw patch · 5 files changed
+11/−15 lines, 5 filesPVP: major bump suggested
API removals or changes: PVP suggests a major version bump
API changes (from Hackage documentation)
- Bio.Data.Bed: _bed :: forall bed_aAp8 a_aAp9 bed_aAAj. Lens (BEDExt bed_aAp8 a_aAp9) (BEDExt bed_aAAj a_aAp9) bed_aAp8 bed_aAAj
+ Bio.Data.Bed: _bed :: forall bed_aAAi a_aAAj bed_aALt. Lens (BEDExt bed_aAAi a_aAAj) (BEDExt bed_aALt a_aAAj) bed_aAAi bed_aALt
- Bio.Data.Bed: _data :: forall bed_aAp8 a_aAp9 a_aAAk. Lens (BEDExt bed_aAp8 a_aAp9) (BEDExt bed_aAp8 a_aAAk) a_aAp9 a_aAAk
+ Bio.Data.Bed: _data :: forall bed_aAAi a_aAAj a_aALu. Lens (BEDExt bed_aAAi a_aAAj) (BEDExt bed_aAAi a_aALu) a_aAAj a_aALu
- Bio.Data.Bed.Types: _bed :: forall bed_aAp8 a_aAp9 bed_aAAj. Lens (BEDExt bed_aAp8 a_aAp9) (BEDExt bed_aAAj a_aAp9) bed_aAp8 bed_aAAj
+ Bio.Data.Bed.Types: _bed :: forall bed_aAAi a_aAAj bed_aALt. Lens (BEDExt bed_aAAi a_aAAj) (BEDExt bed_aALt a_aAAj) bed_aAAi bed_aALt
- Bio.Data.Bed.Types: _data :: forall bed_aAp8 a_aAp9 a_aAAk. Lens (BEDExt bed_aAp8 a_aAp9) (BEDExt bed_aAp8 a_aAAk) a_aAp9 a_aAAk
+ Bio.Data.Bed.Types: _data :: forall bed_aAAi a_aAAj a_aALu. Lens (BEDExt bed_aAAi a_aAAj) (BEDExt bed_aAAi a_aALu) a_aAAj a_aALu
Files
- bioinformatics-toolkit.cabal +1/−1
- src/Bio/Data/Bam.hs +0/−1
- src/Bio/Data/Bed.hs +0/−2
- src/Bio/Data/Bed/Types.hs +10/−10
- src/Bio/RealWorld/ENCODE.hs +0/−1
bioinformatics-toolkit.cabal view
@@ -1,5 +1,5 @@ name: bioinformatics-toolkit-version: 0.9.1+version: 0.9.2 synopsis: A collection of bioinformatics tools description: A collection of bioinformatics tools license: MIT
src/Bio/Data/Bam.hs view
@@ -20,7 +20,6 @@ import Bio.Data.Bed.Types import Bio.Data.Fastq import Bio.HTS-import Bio.HTS.Types (BAM, BAMHeader, SortOrder(..)) import Conduit -- | Convert bam record to bed record. Unmapped reads will be discarded.
src/Bio/Data/Bed.hs view
@@ -53,14 +53,12 @@ import Conduit import Control.Arrow ((***)) import Lens.Micro-import Control.Monad.State.Strict import qualified Data.ByteString.Char8 as B import qualified Data.Foldable as F import Data.Function (on) import qualified Data.HashMap.Strict as M import qualified Data.IntervalMap.Strict as IM import Data.List (groupBy, sortBy, group)-import Data.Ord (comparing) import Data.Conduit.Zlib (gzip, ungzip, multiple) import qualified Data.Vector as V import qualified Data.Vector.Algorithms.Intro as I
src/Bio/Data/Bed/Types.hs view
@@ -31,7 +31,6 @@ import qualified Data.HashMap.Strict as M import qualified Data.IntervalMap.Strict as IM import Data.Maybe (fromJust, fromMaybe)-import Data.Monoid ((<>)) import Bio.Utils.Misc (readDouble, readInt) @@ -209,16 +208,17 @@ instance BEDConvert NarrowPeak where asBed chr s e = NarrowPeak chr s e Nothing 0 Nothing 0 Nothing Nothing Nothing - fromLine l = NarrowPeak a (readInt b) (readInt c)- (if d == "." then Nothing else Just d)- (readInt e)- (if f == "." then Nothing else if f == "+" then Just True else Just False)- (readDouble g)- (readDoubleNonnegative h)- (readDoubleNonnegative i)- (readIntNonnegative j)+ fromLine = go . B.split '\t' where- (a:b:c:d:e:f:g:h:i:j:_) = B.split '\t' l+ go [a,b,c] = convert $ BED3 a (readInt b) $ readInt c+ go (a:b:c:d:e:f:g:h:i:j:_) = NarrowPeak a (readInt b) (readInt c)+ (if d == "." then Nothing else Just d)+ (readInt e)+ (if f == "." then Nothing else if f == "+" then Just True else Just False)+ (readDouble g)+ (readDoubleNonnegative h)+ (readDoubleNonnegative i)+ (readIntNonnegative j) {-# INLINE fromLine #-} toLine (NarrowPeak a b c d e f g h i j) = B.intercalate "\t"
src/Bio/RealWorld/ENCODE.hs view
@@ -35,7 +35,6 @@ import qualified Data.Sequence as S import qualified Data.Text as T import qualified Data.Vector as V-import Data.Semigroup (Semigroup(..)) import Network.HTTP.Conduit import Data.Default.Class