Bio.Location.Position

Data type for a sequence position.

Zero-based Offset / Int64 indices are used throughout, to facilitate direct use of indexing functions on SeqData.

Sequence positions

data Pos

Position in a sequence

Constructors

Pos

Fields

offset :: !Offset

0-based index of the position

strand :: !Strand

Strand of the position

Instances

Eq Pos

Ord Pos

Read Pos

Show Pos

Ix Pos

Stranded Pos

Manipulating positions

slide :: Pos -> Offset -> Pos

Returns a position resulting from sliding the original position along the sequence by a specified offset. A positive offset will move the position away from the 5' end of the forward stand of the sequence regardless of the strand of the position itself. Thus,

 slide (revCompl pos) off == revCompl (slide pos off)

Extracting sequences

seqNt :: (Error e, MonadError e m) => SeqData -> Pos -> m Char

Extract the nucleotide at a specific sequence position. If the position lies outside the bounds of the sequence, an error results.

seqNtPadded :: SeqData -> Pos -> Char

As seqNt, extract the nucleotide at a specific sequence position, but return N when the position lies outside the bounds of the sequence.

 seqNtPadded sequ pos == (either 'N' id . seqNt sequ) pos

Displaying positions

display :: Pos -> String

Display a human-friendly, zero-based representation of a sequence position.