millironx/SequenceVariation.jl
1
0
Fork 0
mirror of https://github.com/MillironX/SequenceVariation.jl.git synced 2024-11-22 05:19:55 +00:00
Code Issues Releases Packages Activity

docs: Add examples of alignment getters

Browse source
This commit is contained in:
Thomas A. Christensen II 2023-04-08 20:44:21 -05:00
parent 341faa45e3
commit 6b2bd018e2
Signed by: millironx
GPG key ID: 09335146883990B9
1 changed files with 18 additions and 0 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

18
docs/src/haplotypes.md
View file

@ -39,6 +39,24 @@ human2 == bovine
human2 == human
```
## Alignment reconstruction
Just like [Sequence reconstruction](@ref), alignments can also be reconstructed
from `Haplotype`s using the extension of the [`BioAlignments.alignment`](@ref)
function.
```@repl call_variants
human_alignment = alignment(bos_human_haplotype)
human_alignment == bos_human_alignment
```
Alternatively, you can get the information in CIGAR format using the
extension of the [`BioAlignments.cigar`](@ref) function.
```@repl call_variants
cigar(bos_human_haplotype)
```
## Reference switching
All variations within a haplotype can be mapped to a new reference sequence