Safe Haskell | None |
---|---|

Language | Haskell98 |

- 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`

.

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).

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

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