Safe Haskell | None |
---|---|
Language | Haskell2010 |
- class BEDLike b where
- class BEDLike b => BEDConvert b where
- data BED = BED {
- _bed_chrom :: !ByteString
- _bed_chromStart :: !Int
- _bed_chromEnd :: !Int
- _bed_name :: !(Maybe ByteString)
- _bed_score :: !(Maybe Double)
- _bed_strand :: !(Maybe Bool)
- data BED3 = BED3 {
- _bed3_chrom :: !ByteString
- _bed3_chrom_start :: !Int
- _bed3_chrom_end :: !Int
- data NarrowPeak = NarrowPeak {}
- npSignal :: Lens' NarrowPeak Double
- npQvalue :: Lens' NarrowPeak (Maybe Double)
- npPvalue :: Lens' NarrowPeak (Maybe Double)
- npPeak :: Lens' NarrowPeak (Maybe Int)
- data BEDExt bed a = BEDExt {}
- _data :: forall bed a a. Lens (BEDExt bed a) (BEDExt bed a) a a
- _bed :: forall bed a bed. Lens (BEDExt bed a) (BEDExt bed a) bed bed
- type BEDTree a = HashMap ByteString (IntervalMap Int a)
Documentation
class BEDLike b where Source #
A class representing BED-like data, e.g., BED3, BED6 and BED12. BED format uses 0-based index (see documentation).
class BEDLike b => BEDConvert b where Source #
asBed :: ByteString -> Int -> Int -> b Source #
Construct bed record from chromsomoe, start location and end location
fromLine :: ByteString -> b Source #
Convert bytestring to bed format
toLine :: b -> ByteString Source #
Convert bed to bytestring
BEDConvert NarrowPeak Source # | |
BEDConvert BED3 Source # | |
BEDConvert BED Source # | |
(Default a, Read a, Show a, BEDConvert bed) => BEDConvert (BEDExt bed a) Source # | |
BED6 format
BED6 format, as described in http://genome.ucsc.edu/FAQ/FAQformat.html#format1.7
BED | |
|
BED3 format
BED3 | |
|
data NarrowPeak Source #
ENCODE narrowPeak format: https://genome.ucsc.edu/FAQ/FAQformat.html#format12
type BEDTree a = HashMap ByteString (IntervalMap Int a) Source #