Bio.Bam.Regions

Documentation

data Region

Constructors

Region

Fields

• refseq :: !Refseq
• start :: !Int
• end :: !Int

Instances

Eq Region

Methods

(==) :: Region -> Region -> Bool

(/=) :: Region -> Region -> Bool

Ord Region

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

Methods

showsPrec :: Int -> Region -> ShowS

show :: Region -> String

showList :: [Region] -> ShowS

newtype Regions

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

Methods

showsPrec :: Int -> Regions -> ShowS

show :: Regions -> String

showList :: [Regions] -> ShowS

newtype Subsequence

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

Methods

showsPrec :: Int -> Subsequence -> ShowS

show :: Subsequence -> String

showList :: [Subsequence] -> ShowS

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)