Safe Haskell | None |
---|---|
Language | Haskell2010 |
Annotate the genomic position
of features or elements. A position
has strand information,
and different ways to encode where a feature is located. The position
points to the first
element (e.g. nucleotide).
Together with the Location
module, it becomes possible to annotate substrings.
Synopsis
- data FwdPosition = FwdPosition {
- _fwdStrand :: !Strand
- _fwdStart :: !(Index 0)
- fwdStrand :: Lens' FwdPosition Strand
- fwdStart :: Lens' FwdPosition (Index 0)
- _FwdPosition :: Iso' FwdPosition (Strand, Index 0)
Documentation
data FwdPosition Source #
During streaming construction, it is possible that we know a feature is on the -
strand, but
the length of the contig is not known yet. In that case, FwdPosition
allows expressing the hit
in the coordinate system of the plus strand. Tools like blast do something similar, and express
locations on the minus as y-x
with y>x
.
0123456789 >--> <--< 9876543210
FwdPosition | Plus-based location. |
|
Instances
_FwdPosition :: Iso' FwdPosition (Strand, Index 0) Source #