From 6b2bd018e2e6b5cdd1817b886d0fbe868305d1f7 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 8 Apr 2023 20:44:21 -0500
Subject: [PATCH] docs: Add examples of alignment getters

---
 docs/src/haplotypes.md | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/docs/src/haplotypes.md b/docs/src/haplotypes.md
index 4694b45..b462dba 100644
--- a/docs/src/haplotypes.md
+++ b/docs/src/haplotypes.md
@@ -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