Bio.Data.Bed

Documentation

class BEDLike b where

A class representing BED-like data, e.g., BED3, BED6 and BED12. BED format uses 0-based index (see documentation).

Minimal complete definition

chrom, chromStart, chromEnd, name, score, strand

Methods

chrom :: Lens' b ByteString

Field lens

chromStart :: Lens' b Int

chromEnd :: Lens' b Int

name :: Lens' b (Maybe ByteString)

score :: Lens' b (Maybe Int)

strand :: Lens' b (Maybe Bool)

size :: b -> Int

Return the size of a bed region.

Instances

BEDLike BEDGraph

Defined in Bio.Data.Bed.Types

Methods

chrom :: Lens' BEDGraph ByteString

chromStart :: Lens' BEDGraph Int

chromEnd :: Lens' BEDGraph Int

name :: Lens' BEDGraph (Maybe ByteString)

score :: Lens' BEDGraph (Maybe Int)

strand :: Lens' BEDGraph (Maybe Bool)

size :: BEDGraph -> Int

BEDLike BED3

Defined in Bio.Data.Bed.Types

Methods

chrom :: Lens' BED3 ByteString

chromStart :: Lens' BED3 Int

chromEnd :: Lens' BED3 Int

name :: Lens' BED3 (Maybe ByteString)

score :: Lens' BED3 (Maybe Int)

strand :: Lens' BED3 (Maybe Bool)

size :: BED3 -> Int

BEDLike BED

Defined in Bio.Data.Bed.Types

Methods

chrom :: Lens' BED ByteString

chromStart :: Lens' BED Int

chromEnd :: Lens' BED Int

name :: Lens' BED (Maybe ByteString)

score :: Lens' BED (Maybe Int)

strand :: Lens' BED (Maybe Bool)

size :: BED -> Int

BEDLike NarrowPeak

Defined in Bio.Data.Bed.Types

Methods

chrom :: Lens' NarrowPeak ByteString

chromStart :: Lens' NarrowPeak Int

chromEnd :: Lens' NarrowPeak Int

name :: Lens' NarrowPeak (Maybe ByteString)

score :: Lens' NarrowPeak (Maybe Int)

strand :: Lens' NarrowPeak (Maybe Bool)

size :: NarrowPeak -> Int

BEDLike BroadPeak

Defined in Bio.Data.Bed.Types

Methods

chrom :: Lens' BroadPeak ByteString

chromStart :: Lens' BroadPeak Int

chromEnd :: Lens' BroadPeak Int

name :: Lens' BroadPeak (Maybe ByteString)

score :: Lens' BroadPeak (Maybe Int)

strand :: Lens' BroadPeak (Maybe Bool)

size :: BroadPeak -> Int

BEDLike bed => BEDLike (BEDExt bed a)

Defined in Bio.Data.Bed.Types

Methods

chrom :: Lens' (BEDExt bed a) ByteString

chromStart :: Lens' (BEDExt bed a) Int

chromEnd :: Lens' (BEDExt bed a) Int

name :: Lens' (BEDExt bed a) (Maybe ByteString)

score :: Lens' (BEDExt bed a) (Maybe Int)

strand :: Lens' (BEDExt bed a) (Maybe Bool)

size :: BEDExt bed a -> Int

class BEDLike b => BEDConvert b where

Minimal complete definition

asBed, fromLine, toLine

Methods

asBed :: ByteString -> Int -> Int -> b

Construct bed record from chromsomoe, start location and end location

fromLine :: ByteString -> b

Convert bytestring to bed format

toLine :: b -> ByteString

Convert bed to bytestring

convert :: BEDLike b' => b' -> b

Instances

BEDConvert BEDGraph

Defined in Bio.Data.Bed.Types

Methods

asBed :: ByteString -> Int -> Int -> BEDGraph

fromLine :: ByteString -> BEDGraph

toLine :: BEDGraph -> ByteString

convert :: BEDLike b' => b' -> BEDGraph

BEDConvert BED3

Defined in Bio.Data.Bed.Types

Methods

asBed :: ByteString -> Int -> Int -> BED3

fromLine :: ByteString -> BED3

toLine :: BED3 -> ByteString

convert :: BEDLike b' => b' -> BED3

BEDConvert BED

Defined in Bio.Data.Bed.Types

Methods

asBed :: ByteString -> Int -> Int -> BED

fromLine :: ByteString -> BED

toLine :: BED -> ByteString

convert :: BEDLike b' => b' -> BED

BEDConvert NarrowPeak

Defined in Bio.Data.Bed.Types

Methods

asBed :: ByteString -> Int -> Int -> NarrowPeak

fromLine :: ByteString -> NarrowPeak

toLine :: NarrowPeak -> ByteString

convert :: BEDLike b' => b' -> NarrowPeak

BEDConvert BroadPeak

Defined in Bio.Data.Bed.Types

Methods

asBed :: ByteString -> Int -> Int -> BroadPeak

fromLine :: ByteString -> BroadPeak

toLine :: BroadPeak -> ByteString

convert :: BEDLike b' => b' -> BroadPeak

(Read a, Show a, BEDConvert bed) => BEDConvert (BEDExt bed a)

Defined in Bio.Data.Bed.Types

Methods

asBed :: ByteString -> Int -> Int -> BEDExt bed a

fromLine :: ByteString -> BEDExt bed a

toLine :: BEDExt bed a -> ByteString

convert :: BEDLike b' => b' -> BEDExt bed a

data BED

BED6 format, as described in http://genome.ucsc.edu/FAQ/FAQformat.html#format1.7

Constructors

BED

Fields

• _bed_chrom :: ByteString
• _bed_chromStart :: Int
• _bed_chromEnd :: Int
• _bed_name :: Maybe ByteString
• _bed_score :: Maybe Int
• _bed_strand :: Maybe Bool

  True: "+", False: "-"

Instances

Eq BED

Defined in Bio.Data.Bed.Types

Methods

(==) :: BED -> BED -> Bool

(/=) :: BED -> BED -> Bool

Ord BED

Defined in Bio.Data.Bed.Types

Methods

compare :: BED -> BED -> Ordering

(<) :: BED -> BED -> Bool

(<=) :: BED -> BED -> Bool

(>) :: BED -> BED -> Bool

(>=) :: BED -> BED -> Bool

max :: BED -> BED -> BED

min :: BED -> BED -> BED

Read BED

Defined in Bio.Data.Bed.Types

Methods

readsPrec :: Int -> ReadS BED

readList :: ReadS [BED]

readPrec :: ReadPrec BED

readListPrec :: ReadPrec [BED]

Show BED

Defined in Bio.Data.Bed.Types

Methods

showsPrec :: Int -> BED -> ShowS

show :: BED -> String

showList :: [BED] -> ShowS

Generic BED

Defined in Bio.Data.Bed.Types

Associated Types

type Rep BED :: Type -> Type

Methods

from :: BED -> Rep BED x

to :: Rep BED x -> BED

NFData BED

Defined in Bio.Data.Bed.Types

Methods

rnf :: BED -> ()

BEDConvert BED

Defined in Bio.Data.Bed.Types

Methods

asBed :: ByteString -> Int -> Int -> BED

fromLine :: ByteString -> BED

toLine :: BED -> ByteString

convert :: BEDLike b' => b' -> BED

BEDLike BED

Defined in Bio.Data.Bed.Types

Methods

chrom :: Lens' BED ByteString

chromStart :: Lens' BED Int

chromEnd :: Lens' BED Int

name :: Lens' BED (Maybe ByteString)

score :: Lens' BED (Maybe Int)

strand :: Lens' BED (Maybe Bool)

size :: BED -> Int

type Rep BED

Defined in Bio.Data.Bed.Types

type Rep BED = D1 ('MetaData "BED" "Bio.Data.Bed.Types" "bioinformatics-toolkit-0.10.0-A8Y5r7ZpZ9gGDfktm9e6ZK" 'False) (C1 ('MetaCons "BED" 'PrefixI 'True) ((S1 ('MetaSel ('Just "_bed_chrom") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 ByteString) :*: (S1 ('MetaSel ('Just "_bed_chromStart") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int) :*: S1 ('MetaSel ('Just "_bed_chromEnd") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int))) :*: (S1 ('MetaSel ('Just "_bed_name") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe ByteString)) :*: (S1 ('MetaSel ('Just "_bed_score") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe Int)) :*: S1 ('MetaSel ('Just "_bed_strand") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe Bool))))))

data BED3

BED3 format

Constructors

BED3

Fields

• _bed3_chrom :: ByteString
• _bed3_chrom_start :: Int
• _bed3_chrom_end :: Int

Instances

Eq BED3

Defined in Bio.Data.Bed.Types

Methods

(==) :: BED3 -> BED3 -> Bool

(/=) :: BED3 -> BED3 -> Bool

Ord BED3

Defined in Bio.Data.Bed.Types

Methods

compare :: BED3 -> BED3 -> Ordering

(<) :: BED3 -> BED3 -> Bool

(<=) :: BED3 -> BED3 -> Bool

(>) :: BED3 -> BED3 -> Bool

(>=) :: BED3 -> BED3 -> Bool

max :: BED3 -> BED3 -> BED3

min :: BED3 -> BED3 -> BED3

Read BED3

Defined in Bio.Data.Bed.Types

Methods

readsPrec :: Int -> ReadS BED3

readList :: ReadS [BED3]

readPrec :: ReadPrec BED3

readListPrec :: ReadPrec [BED3]

Show BED3

Defined in Bio.Data.Bed.Types

Methods

showsPrec :: Int -> BED3 -> ShowS

show :: BED3 -> String

showList :: [BED3] -> ShowS

Generic BED3

Defined in Bio.Data.Bed.Types

Associated Types

type Rep BED3 :: Type -> Type

Methods

from :: BED3 -> Rep BED3 x

to :: Rep BED3 x -> BED3

NFData BED3

Defined in Bio.Data.Bed.Types

Methods

rnf :: BED3 -> ()

BEDConvert BED3

Defined in Bio.Data.Bed.Types

Methods

asBed :: ByteString -> Int -> Int -> BED3

fromLine :: ByteString -> BED3

toLine :: BED3 -> ByteString

convert :: BEDLike b' => b' -> BED3

BEDLike BED3

Defined in Bio.Data.Bed.Types

Methods

chrom :: Lens' BED3 ByteString

chromStart :: Lens' BED3 Int

chromEnd :: Lens' BED3 Int

name :: Lens' BED3 (Maybe ByteString)

score :: Lens' BED3 (Maybe Int)

strand :: Lens' BED3 (Maybe Bool)

size :: BED3 -> Int

type Rep BED3

Defined in Bio.Data.Bed.Types

type Rep BED3 = D1 ('MetaData "BED3" "Bio.Data.Bed.Types" "bioinformatics-toolkit-0.10.0-A8Y5r7ZpZ9gGDfktm9e6ZK" 'False) (C1 ('MetaCons "BED3" 'PrefixI 'True) (S1 ('MetaSel ('Just "_bed3_chrom") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 ByteString) :*: (S1 ('MetaSel ('Just "_bed3_chrom_start") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int) :*: S1 ('MetaSel ('Just "_bed3_chrom_end") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int))))

data BEDGraph

Bedgraph format.

Constructors

BEDGraph

Fields

• _bdg_chrom :: ByteString
• _bdg_chrom_start :: Int
• _bdg_chrom_end :: Int
• _bdg_value :: Double

Instances

Eq BEDGraph

Defined in Bio.Data.Bed.Types

Methods

(==) :: BEDGraph -> BEDGraph -> Bool

(/=) :: BEDGraph -> BEDGraph -> Bool

Ord BEDGraph

Defined in Bio.Data.Bed.Types

Methods

compare :: BEDGraph -> BEDGraph -> Ordering

(<) :: BEDGraph -> BEDGraph -> Bool

(<=) :: BEDGraph -> BEDGraph -> Bool

(>) :: BEDGraph -> BEDGraph -> Bool

(>=) :: BEDGraph -> BEDGraph -> Bool

max :: BEDGraph -> BEDGraph -> BEDGraph

min :: BEDGraph -> BEDGraph -> BEDGraph

Read BEDGraph

Defined in Bio.Data.Bed.Types

Methods

readsPrec :: Int -> ReadS BEDGraph

readList :: ReadS [BEDGraph]

readPrec :: ReadPrec BEDGraph

readListPrec :: ReadPrec [BEDGraph]

Show BEDGraph

Defined in Bio.Data.Bed.Types

Methods

showsPrec :: Int -> BEDGraph -> ShowS

show :: BEDGraph -> String

showList :: [BEDGraph] -> ShowS

Generic BEDGraph

Defined in Bio.Data.Bed.Types

Associated Types

type Rep BEDGraph :: Type -> Type

Methods

from :: BEDGraph -> Rep BEDGraph x

to :: Rep BEDGraph x -> BEDGraph

NFData BEDGraph

Defined in Bio.Data.Bed.Types

Methods

rnf :: BEDGraph -> ()

BEDConvert BEDGraph

Defined in Bio.Data.Bed.Types

Methods

asBed :: ByteString -> Int -> Int -> BEDGraph

fromLine :: ByteString -> BEDGraph

toLine :: BEDGraph -> ByteString

convert :: BEDLike b' => b' -> BEDGraph

BEDLike BEDGraph

Defined in Bio.Data.Bed.Types

Methods

chrom :: Lens' BEDGraph ByteString

chromStart :: Lens' BEDGraph Int

chromEnd :: Lens' BEDGraph Int

name :: Lens' BEDGraph (Maybe ByteString)

score :: Lens' BEDGraph (Maybe Int)

strand :: Lens' BEDGraph (Maybe Bool)

size :: BEDGraph -> Int

type Rep BEDGraph

Defined in Bio.Data.Bed.Types

type Rep BEDGraph = D1 ('MetaData "BEDGraph" "Bio.Data.Bed.Types" "bioinformatics-toolkit-0.10.0-A8Y5r7ZpZ9gGDfktm9e6ZK" 'False) (C1 ('MetaCons "BEDGraph" 'PrefixI 'True) ((S1 ('MetaSel ('Just "_bdg_chrom") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 ByteString) :*: S1 ('MetaSel ('Just "_bdg_chrom_start") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int)) :*: (S1 ('MetaSel ('Just "_bdg_chrom_end") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int) :*: S1 ('MetaSel ('Just "_bdg_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Double))))

bdgValue :: Lens' BEDGraph Double

data NarrowPeak

ENCODE narrowPeak format: https://genome.ucsc.edu/FAQ/FAQformat.html#format12

Constructors

NarrowPeak

Fields

• _npChrom :: ByteString
• _npStart :: Int
• _npEnd :: Int
• _npName :: Maybe ByteString
• _npScore :: Int
• _npStrand :: Maybe Bool
• _npSignal :: Double
• _npPvalue :: Maybe Double
• _npQvalue :: Maybe Double
• _npPeak :: Maybe Int

Instances

Eq NarrowPeak

Defined in Bio.Data.Bed.Types

Methods

(==) :: NarrowPeak -> NarrowPeak -> Bool

(/=) :: NarrowPeak -> NarrowPeak -> Bool

Read NarrowPeak

Defined in Bio.Data.Bed.Types

Methods

readsPrec :: Int -> ReadS NarrowPeak

readList :: ReadS [NarrowPeak]

readPrec :: ReadPrec NarrowPeak

readListPrec :: ReadPrec [NarrowPeak]

Show NarrowPeak

Defined in Bio.Data.Bed.Types

Methods

showsPrec :: Int -> NarrowPeak -> ShowS

show :: NarrowPeak -> String

showList :: [NarrowPeak] -> ShowS

Generic NarrowPeak

Defined in Bio.Data.Bed.Types

Associated Types

type Rep NarrowPeak :: Type -> Type

Methods

from :: NarrowPeak -> Rep NarrowPeak x

to :: Rep NarrowPeak x -> NarrowPeak

NFData NarrowPeak

Defined in Bio.Data.Bed.Types

Methods

rnf :: NarrowPeak -> ()

BEDConvert NarrowPeak

Defined in Bio.Data.Bed.Types

Methods

asBed :: ByteString -> Int -> Int -> NarrowPeak

fromLine :: ByteString -> NarrowPeak

toLine :: NarrowPeak -> ByteString

convert :: BEDLike b' => b' -> NarrowPeak

BEDLike NarrowPeak

Defined in Bio.Data.Bed.Types

Methods

chrom :: Lens' NarrowPeak ByteString

chromStart :: Lens' NarrowPeak Int

chromEnd :: Lens' NarrowPeak Int

name :: Lens' NarrowPeak (Maybe ByteString)

score :: Lens' NarrowPeak (Maybe Int)

strand :: Lens' NarrowPeak (Maybe Bool)

size :: NarrowPeak -> Int

type Rep NarrowPeak

Defined in Bio.Data.Bed.Types

type Rep NarrowPeak = D1 ('MetaData "NarrowPeak" "Bio.Data.Bed.Types" "bioinformatics-toolkit-0.10.0-A8Y5r7ZpZ9gGDfktm9e6ZK" 'False) (C1 ('MetaCons "NarrowPeak" 'PrefixI 'True) (((S1 ('MetaSel ('Just "_npChrom") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 ByteString) :*: S1 ('MetaSel ('Just "_npStart") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int)) :*: (S1 ('MetaSel ('Just "_npEnd") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int) :*: (S1 ('MetaSel ('Just "_npName") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe ByteString)) :*: S1 ('MetaSel ('Just "_npScore") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int)))) :*: ((S1 ('MetaSel ('Just "_npStrand") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe Bool)) :*: S1 ('MetaSel ('Just "_npSignal") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Double)) :*: (S1 ('MetaSel ('Just "_npPvalue") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe Double)) :*: (S1 ('MetaSel ('Just "_npQvalue") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe Double)) :*: S1 ('MetaSel ('Just "_npPeak") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe Int)))))))

npSignal :: Lens' NarrowPeak Double

npPvalue :: Lens' NarrowPeak (Maybe Double)

npQvalue :: Lens' NarrowPeak (Maybe Double)

npPeak :: Lens' NarrowPeak (Maybe Int)

data BEDExt bed a

Constructors

BEDExt

Fields

• _ext_bed :: bed
• _ext_data :: a

Instances

(Eq bed, Eq a) => Eq (BEDExt bed a)

Defined in Bio.Data.Bed.Types

Methods

(==) :: BEDExt bed a -> BEDExt bed a -> Bool

(/=) :: BEDExt bed a -> BEDExt bed a -> Bool

(Read bed, Read a) => Read (BEDExt bed a)

Defined in Bio.Data.Bed.Types

Methods

readsPrec :: Int -> ReadS (BEDExt bed a)

readList :: ReadS [BEDExt bed a]

readPrec :: ReadPrec (BEDExt bed a)

readListPrec :: ReadPrec [BEDExt bed a]

(Show bed, Show a) => Show (BEDExt bed a)

Defined in Bio.Data.Bed.Types

Methods

showsPrec :: Int -> BEDExt bed a -> ShowS

show :: BEDExt bed a -> String

showList :: [BEDExt bed a] -> ShowS

Generic (BEDExt bed a)

Defined in Bio.Data.Bed.Types

Associated Types

type Rep (BEDExt bed a) :: Type -> Type

Methods

from :: BEDExt bed a -> Rep (BEDExt bed a) x

to :: Rep (BEDExt bed a) x -> BEDExt bed a

(NFData bed, NFData a) => NFData (BEDExt bed a)

Defined in Bio.Data.Bed.Types

Methods

rnf :: BEDExt bed a -> ()

(Read a, Show a, BEDConvert bed) => BEDConvert (BEDExt bed a)

Defined in Bio.Data.Bed.Types

Methods

asBed :: ByteString -> Int -> Int -> BEDExt bed a

fromLine :: ByteString -> BEDExt bed a

toLine :: BEDExt bed a -> ByteString

convert :: BEDLike b' => b' -> BEDExt bed a

BEDLike bed => BEDLike (BEDExt bed a)

Defined in Bio.Data.Bed.Types

Methods

chrom :: Lens' (BEDExt bed a) ByteString

chromStart :: Lens' (BEDExt bed a) Int

chromEnd :: Lens' (BEDExt bed a) Int

name :: Lens' (BEDExt bed a) (Maybe ByteString)

score :: Lens' (BEDExt bed a) (Maybe Int)

strand :: Lens' (BEDExt bed a) (Maybe Bool)

size :: BEDExt bed a -> Int

type Rep (BEDExt bed a)

Defined in Bio.Data.Bed.Types

type Rep (BEDExt bed a) = D1 ('MetaData "BEDExt" "Bio.Data.Bed.Types" "bioinformatics-toolkit-0.10.0-A8Y5r7ZpZ9gGDfktm9e6ZK" 'False) (C1 ('MetaCons "BEDExt" 'PrefixI 'True) (S1 ('MetaSel ('Just "_ext_bed") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 bed) :*: S1 ('MetaSel ('Just "_ext_data") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 a)))

_bed :: forall bed a bed. Lens (BEDExt bed a) (BEDExt bed a) bed bed

_data :: forall bed a a. Lens (BEDExt bed a) (BEDExt bed a) a a

type BEDTree a = HashMap ByteString (IntervalMap Int a)

bedToTree :: BEDLike b => (a -> a -> a) -> [(b, a)] -> BEDTree a

sortedBedToTree :: (BEDLike b, Foldable f) => (a -> a -> a) -> Sorted (f (b, a)) -> BEDTree a

Convert a set of sorted bed records to interval tree, with combining function for equal keys.

queryIntersect :: BEDLike b => b -> BEDTree a -> [(BED3, a)]

intersecting :: BEDLike b => BEDTree a -> b -> IntervalMap Int a

isIntersected :: BEDLike b => BEDTree a -> b -> Bool

sizeOverlapped :: (BEDLike b1, BEDLike b2) => b1 -> b2 -> Int

splitBed :: BEDConvert b => Int -> b -> [b]

split a bed region into k consecutive subregions, discarding leftovers

splitBedBySize :: BEDConvert b => Int -> b -> [b]

split a bed region into consecutive fixed size subregions, discarding leftovers

splitBedBySizeLeft :: BEDConvert b => Int -> b -> [b]

split a bed region into consecutive fixed size subregions, including leftovers

splitBedBySizeOverlap

Arguments

:: BEDConvert b

=> Int

bin size

-> Int

overlap size

-> b

-> [b]

sortBed :: BEDLike b => [b] -> Sorted (Vector b)

sort BED, first by chromosome (alphabetical order), then by chromStart, last by chromEnd

intersectBed :: (BEDLike b1, BEDLike b2, Monad m) => [b2] -> ConduitT b1 b1 m ()

return records in A that are overlapped with records in B

intersectBedWith :: (BEDLike b1, BEDLike b2, Monad m) => (b1 -> [b2] -> a) -> [b2] -> ConduitT b1 a m ()

intersectSortedBed :: (BEDLike b1, BEDLike b2, Monad m) => Sorted (Vector b2) -> ConduitT b1 b1 m ()

return records in A that are overlapped with records in B

intersectSortedBedWith :: (BEDLike b1, BEDLike b2, Monad m) => (b1 -> [b2] -> a) -> Sorted (Vector b2) -> ConduitT b1 a m ()

isOverlapped :: (BEDLike b1, BEDLike b2) => b1 -> b2 -> Bool

mergeBed :: (BEDConvert b, Monad m) => [b] -> ConduitT i b m ()

Merge overlapping regions.

mergeBedWith :: (BEDLike b, Monad m) => ([b] -> a) -> [b] -> ConduitT i a m ()

Merge overlapping regions according to a merging function.

mergeSortedBed :: (BEDConvert b, Monad m) => ConduitT b b m ()

Merge overlapping regions. The input stream must be sorted first.

mergeSortedBedWith :: (BEDLike b, Monad m) => ([b] -> a) -> ConduitT b a m ()

Merge overlapping regions according to a merging function. The input stream must be sorted first.

countOverlapped :: BEDLike b => [b] -> [(BED3, Int)]

Split overlapped regions into non-overlapped regions. The input must be overlapped. This function is usually used with mergeBedWith.

IO

streamBed :: (MonadResource m, BEDConvert b, MonadIO m) => FilePath -> ConduitT i b m ()

streamBedGzip :: (BEDConvert b, MonadResource m, MonadThrow m, PrimMonad m) => FilePath -> ConduitT i b m ()

readBed :: BEDConvert b => FilePath -> IO [b]

sinkFileBed :: (BEDConvert b, MonadResource m) => FilePath -> ConduitT b o m ()

sinkFileBedGzip :: (BEDConvert b, MonadResource m, MonadThrow m, PrimMonad m) => FilePath -> ConduitT b o m ()

sinkHandleBed :: (BEDConvert b, MonadIO m) => Handle -> ConduitT b o m ()

writeBed :: BEDConvert b => FilePath -> [b] -> IO ()

compareBed :: (BEDLike b1, BEDLike b2) => b1 -> b2 -> Ordering

Compare bed records using only the chromosome, start and end positions. Unlike the `compare' from the Ord type class, this function can compare different types of BED data types.