Safe Haskell	None
Language	Haskell98

Bio.Bam.Regions

Synopsis

Documentation

data Region Source

Constructors

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

Instances

Eq Region Source
Ord Region Source
Show Region Source

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

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

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