- newtype Loc = Loc [ContigLoc]
- bounds :: Loc -> (Offset, Offset)
- length :: Loc -> Offset
- startPos :: Loc -> Pos
- endPos :: Loc -> Pos
- posInto :: Pos -> Loc -> Maybe Pos
- posOutof :: Pos -> Loc -> Maybe Pos
- isWithin :: Pos -> Loc -> Bool
- overlaps :: Loc -> Loc -> Bool
- seqData :: (Error e, MonadError e m) => SeqData -> Loc -> m SeqData
- seqDataPadded :: SeqData -> Loc -> SeqData
- extend :: (Offset, Offset) -> Loc -> Loc
- display :: Loc -> String
General (disjoint) sequence region consisting of a concatenated
set of contiguous regions (see
Locations and positions
The bounds of a sequence location. This is a pair consisting of the lowest and highest sequence offsets covered by the region. The bounds ignore the strand of the sequence location, and the first element of the pair will always be lower than the second. Even if the positions in the location do not run monotonically through the location, the overall lowest and highest sequence offsets are returned.
Given a sequence position and a sequence location relative to the
same sequence, compute a new position representing the original
position relative to the subsequence defined by the location. If
the sequence position lies outside of the sequence location,
Nothing is returned; thus, the offset of the new position will
always be in the range
[0, length cloc - 1].
When the sequence positions in the location are not monotonic, there may be multiple possible posInto solutions. That is, if the same outer sequence position is covered by two different contiguous blocks of the location, then it would have two possible sequence positions relative to the location. In this case, the position 5'-most in the location orientation is returned.
Given a sequence location and a sequence position within that
location, compute a new position representing the original position
relative to the outer sequence. If the sequence position lies
outside the location,
Nothing is returned.
This function inverts
posInto when the sequence position lies
within the position is actually within the location. Due to the
possibility of redundant location-relative positions for a given
posInto does not necessary invert
True when a sequence position lies within a sequence
location on the same sequence, and occupies the same strand.
True when two sequence locations overlap at any
Extract the nucleotide
SeqData for the sequence location. If
any part of the location lies outside the bounds of the sequence,
an error results.
seqData, extract the nucleotide subsequence for the
location. Any positions in the location lying outside the bounds
of the sequence are returned as
N rather than producing an error.
Returns a sequence location produced by extending the original
location on each end, based on a pair of (5\' extension, /3'
extension/). These add contiguous positions to the 5' and 3'
ends of the original location. The 5' extension is applied to the
5' end of the location on the location strand; if the location is
RevCompl strand, the 5' end will have a higher offset
than the 3' end and this offset will increase by the amount of the
5' extension. Similarly, the 3' extension is applied to the 3'
end of the location.