Bio.Data.Bed.Types

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 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 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 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 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 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 BroadPeak

Defined in Bio.Data.Bed.Types

Methods

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

fromLine :: ByteString -> BroadPeak

toLine :: BroadPeak -> ByteString

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

(Default 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

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

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

data BED3

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

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

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

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

npSignal :: Lens' NarrowPeak Double

npPvalue :: Lens' NarrowPeak (Maybe Double)

npQvalue :: Lens' NarrowPeak (Maybe Double)

npPeak :: Lens' NarrowPeak (Maybe Int)

data BroadPeak

ENCODE broadPeak format: https://genome.ucsc.edu/FAQ/FAQformat.html#format13

Constructors

BroadPeak

Fields

• _bpChrom :: !ByteString
• _bpStart :: !Int
• _bpEnd :: !Int
• _bpName :: !(Maybe ByteString)
• _bpScore :: !Int
• _bpStrand :: !(Maybe Bool)
• _bpSignal :: !Double
• _bpPvalue :: !(Maybe Double)
• _bpQvalue :: !(Maybe Double)

Instances

Eq BroadPeak

Defined in Bio.Data.Bed.Types

Methods

(==) :: BroadPeak -> BroadPeak -> Bool

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

Read BroadPeak

Defined in Bio.Data.Bed.Types

Methods

readsPrec :: Int -> ReadS BroadPeak

readList :: ReadS [BroadPeak]

readPrec :: ReadPrec BroadPeak

readListPrec :: ReadPrec [BroadPeak]

Show BroadPeak

Defined in Bio.Data.Bed.Types

Methods

showsPrec :: Int -> BroadPeak -> ShowS

show :: BroadPeak -> String

showList :: [BroadPeak] -> ShowS

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

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

bpSignal :: Lens' BroadPeak Double

bpPvalue :: Lens' BroadPeak (Maybe Double)

bpQvalue :: Lens' BroadPeak (Maybe Double)

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

(Default 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

_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)

newtype Sorted b

a type to imply that underlying data structure is sorted

Constructors

Sorted

Fields

• fromSorted :: b

Instances

Eq b => Eq (Sorted b)

Defined in Bio.Data.Bed.Types

Methods

(==) :: Sorted b -> Sorted b -> Bool

(/=) :: Sorted b -> Sorted b -> Bool

Read b => Read (Sorted b)

Defined in Bio.Data.Bed.Types

Methods

readsPrec :: Int -> ReadS (Sorted b)

readList :: ReadS [Sorted b]

readPrec :: ReadPrec (Sorted b)

readListPrec :: ReadPrec [Sorted b]

Show b => Show (Sorted b)

Defined in Bio.Data.Bed.Types

Methods

showsPrec :: Int -> Sorted b -> ShowS

show :: Sorted b -> String

showList :: [Sorted b] -> ShowS