- data ContigLoc = ContigLoc {}
- fromStartEnd :: Offset -> Offset -> ContigLoc
- fromPosLen :: Pos -> Offset -> ContigLoc
- bounds :: ContigLoc -> (Offset, Offset)
- startPos :: ContigLoc -> Pos
- endPos :: ContigLoc -> Pos
- posInto :: Pos -> ContigLoc -> Maybe Pos
- posOutof :: Pos -> ContigLoc -> Maybe Pos
- isWithin :: Pos -> ContigLoc -> Bool
- overlaps :: ContigLoc -> ContigLoc -> Bool
- seqData :: (Error e, MonadError e m) => SeqData -> ContigLoc -> m SeqData
- seqDataPadded :: SeqData -> ContigLoc -> SeqData
- slide :: Offset -> ContigLoc -> ContigLoc
- extend :: (Offset, Offset) -> ContigLoc -> ContigLoc
- display :: ContigLoc -> String
Sequence locations
Contiguous sequence location defined by a span of sequence positions, lying on a specific strand of the sequence.
fromStartEnd :: Offset -> Offset -> ContigLocSource
Create a sequence location lying between 0-based starting and
ending offsets. When start < end
, the location
be on the forward strand, otherwise it will be on the
reverse complement strand.
fromPosLen :: Pos -> Offset -> ContigLocSource
Create a sequence location from the sequence position of the start of the location and the length of the position. The strand of the location, and the direction it extends from the starting position, are determined by the strand of the starting position.
Locations and positions
bounds :: ContigLoc -> (Offset, Offset)Source
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.
endPos :: ContigLoc -> PosSource
Sequence position of the end of the location, as described in startPos
.
posInto :: Pos -> ContigLoc -> Maybe PosSource
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]
.
posOutof :: Pos -> ContigLoc -> Maybe PosSource
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.
isWithin :: Pos -> ContigLoc -> BoolSource
Returns True
when a sequence position lies within a sequence
location on the same sequence, and occupies the same strand.
overlaps :: ContigLoc -> ContigLoc -> BoolSource
Returns True
when two sequence locations overlap at any
position.
Extracting subsequences
seqData :: (Error e, MonadError e m) => SeqData -> ContigLoc -> m SeqDataSource
Extract the nucleotide SeqData
for the sequence location. If
any part of the location lies outside the bounds of the sequence,
an error results.
seqDataPadded :: SeqData -> ContigLoc -> SeqDataSource
As 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.
Transforming locations
slide :: Offset -> ContigLoc -> ContigLocSource
Returns a location resulting from sliding the original location along the sequence by a specified offset. A positive offset will move the location away from the 5' end of the forward stand of the sequence regardless of the strand of the location itself. Thus,
slide (revCompl cloc) off == revCompl (slide cloc off)
extend :: (Offset, Offset) -> ContigLoc -> ContigLocSource
Returns a sequence location produced by extending the original
location on each end, based on a pair of (5\' extension, /3'
extension/). The 5' extension is applied to the 5' end of the
location on the location strand; if the location is on the
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.