Safe Haskell	None
Language	Haskell2010

Bio.Bam.Regions

Synopsis

Documentation

data Region Source #

Constructors

Region
Fields refseq :: !Refseq start :: !Int end :: !Int

Instances

Eq Region Source #
Methods (==) :: Region -> Region -> Bool # (/=) :: Region -> Region -> Bool #
Ord Region Source #
Methods compare :: Region -> Region -> Ordering # (<) :: Region -> Region -> Bool # (<=) :: Region -> Region -> Bool # (>) :: Region -> Region -> Bool # (>=) :: Region -> Region -> Bool # max :: Region -> Region -> Region # min :: Region -> Region -> Region #
Show Region Source #
Methods showsPrec :: Int -> Region -> ShowS # show :: Region -> String # showList :: [Region] -> ShowS #

newtype Regions Source #

A subset of a genome. The idea is to map the reference sequence (represented by its number) to a Subseqeunce.

Constructors

Regions (IntMap Subsequence)

Instances

Show Regions Source #
Methods showsPrec :: Int -> Regions -> ShowS # show :: Regions -> String # showList :: [Regions] -> ShowS #

newtype Subsequence Source #

A mostly contiguous subset of a sequence, stored as a set of non-overlapping intervals in an IntMap from start position to end position (half-open intervals, naturally).

Constructors

Subsequence (IntMap Int)

Instances

Show Subsequence Source #
Methods showsPrec :: Int -> Subsequence -> ShowS # show :: Subsequence -> String # showList :: [Subsequence] -> ShowS #

toList :: Regions -> [(Refseq, Subsequence)] Source #

fromList :: [Region] -> Regions Source #

add :: Region -> Regions -> Regions Source #

addInt :: Int -> Int -> Subsequence -> Subsequence Source #

overlaps :: Int -> Int -> Subsequence -> Bool Source #

lookupLT :: Key -> IntMap a -> Maybe (Key, a) Source #