| Safe Haskell | None |
|---|---|
| Language | Haskell2010 |
Bio.Bam.Regions
- data Region = Region {}
- newtype Regions = Regions (IntMap Subsequence)
- newtype Subsequence = Subsequence (IntMap Int)
- toList :: Regions -> [(Refseq, Subsequence)]
- fromList :: [Region] -> Regions
- add :: Region -> Regions -> Regions
- addInt :: Int -> Int -> Subsequence -> Subsequence
- overlaps :: Int -> Int -> Subsequence -> Bool
- lookupLT :: Key -> IntMap a -> Maybe (Key, a)
Documentation
A subset of a genome. The idea is to map the reference sequence
(represented by its number) to a Subseqeunce.
Constructors
| Regions (IntMap Subsequence) |
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
addInt :: Int -> Int -> Subsequence -> Subsequence Source
overlaps :: Int -> Int -> Subsequence -> Bool Source