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docs: Add examples of alignment getters

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Thomas A. Christensen II 2023-04-08 20:44:21 -05:00
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docs/src/haplotypes.md
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@ -39,6 +39,24 @@ human2 == bovine
human2 == human 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 ## Reference switching
All variations within a haplotype can be mapped to a new reference sequence All variations within a haplotype can be mapped to a new reference sequence