bio-0.3.5: A bioinformatics library Source code Contents Index

Bio.Location.ContigLocation

Description

Data types for working with locations in a sequence. Zero-based Int64 indices are used throughout, to facilitate direct use of indexing functions on SeqData.

Synopsis

data ContigLoc = ContigLoc { offset5 :: !Offset length :: !Offset strand :: !Strand } fromStartEnd :: Offset -> Offset -> ContigLoc fromPosLen :: Pos -> Offset -> ContigLoc bounds :: ContigLoc -> (Offset, Offset) startPos :: ContigLoc -> Pos endPos :: ContigLoc -> Pos slide :: Offset -> ContigLoc -> ContigLoc extend :: (Offset, Offset) -> ContigLoc -> ContigLoc posInto :: Pos -> ContigLoc -> Maybe Pos posOutof :: Pos -> ContigLoc -> Maybe Pos seqData :: (Error e, MonadError e m) => SeqData -> ContigLoc -> m SeqData seqDataPadded :: SeqData -> ContigLoc -> SeqData isWithin :: Pos -> ContigLoc -> Bool overlaps :: ContigLoc -> ContigLoc -> Bool display :: ContigLoc -> String

Documentation

data ContigLoc Source

Contiguous set of positions in a sequence Constructors ContigLoc offset5 :: !Offset 5' end of region on target sequence, 0-based index length :: !Offset length of region on target sequence strand :: !Strand strand of region Instances Eq ContigLoc Ord ContigLoc Show ContigLoc Stranded ContigLoc

fromStartEnd :: Offset -> Offset -> ContigLoc Source

Create a ContigLoc from 0-based starting and ending positions. When start is less than end the position will be on the Fwd Strand, otherwise it will be on the RevCompl strand.

fromPosLen :: Pos -> Offset -> ContigLoc Source

Create a ContigLoc from a Pos.Pos defining the start (ContigLoc 5 prime end) position on the sequence and the length.

bounds :: ContigLoc -> (Offset, Offset) Source

The bounds of a ContigLoc, a pair of the lowest and highest sequence indices covered by the region, which ignores the strand of the ContigLoc. The first element of the pair will always be lower than the second.

startPos :: ContigLoc -> Pos Source

0-based starting (5' in the region orientation) position

endPos :: ContigLoc -> Pos Source

0-based ending (3' in the region orientation) position

slide :: Offset -> ContigLoc -> ContigLoc Source

Move a ContigLoc region by a specified offset

extend :: (Offset, Offset) -> ContigLoc -> ContigLoc Source

ContigLoc extended on the 5' and 3' ends.

posInto :: Pos -> ContigLoc -> Maybe Pos Source

For a Pos and a ContigLoc on the same sequence, find the corresponding Pos relative to the ContigLoc, provided it is within the ContigLoc.

posOutof :: Pos -> ContigLoc -> Maybe Pos Source

For a Pos specified relative to a ContigLoc, find the corresponding Pos relative to the outer sequence, provided that the Pos is within the bounds of the ContigLoc.

seqData :: (Error e, MonadError e m) => SeqData -> ContigLoc -> m SeqData Source

Subsequence SeqData for a ContigLoc, provided that the region is entirely within the sequence.

seqDataPadded :: SeqData -> ContigLoc -> SeqData Source

Subsequence SeqData for a ContigLoc, padded as needed with Ns

isWithin :: Pos -> ContigLoc -> Bool Source

For a Pos and a ContigLoc on the same sequence, is the Pos within the ContigLoc.

overlaps :: ContigLoc -> ContigLoc -> Bool Source

For a pair of ContigLoc regions on the same sequence, indicates if they overlap at all.

display :: ContigLoc -> String Source

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