From ecaa995d2b63d82117f44f192298cf32d7887596 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 5 Jan 2023 13:10:24 -0600
Subject: [PATCH] Update API documentation for different `translate` methods

---
 docs/src/api.md        | 3 ++-
 docs/src/variations.md | 6 ++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/docs/src/api.md b/docs/src/api.md
index 8dcb67a..ef8121e 100644
--- a/docs/src/api.md
+++ b/docs/src/api.md
@@ -22,6 +22,7 @@ Haplotype
 reference(::Haplotype)
 variations
 reconstruct
+translate(::Haplotype{S,T}, ::PairwiseAlignment{S,S}) where {S,T}
 ```
 
 ## Variations
@@ -30,7 +31,7 @@ reconstruct
 Variation
 reference(::Variation)
 mutation
-translate
+translate(::Variation{S,T}, ::PairwiseAlignment{S,S}) where {S,T}
 refbases
 altbases
 ```
diff --git a/docs/src/variations.md b/docs/src/variations.md
index 46d2e79..8397c20 100644
--- a/docs/src/variations.md
+++ b/docs/src/variations.md
@@ -54,13 +54,15 @@ variations(bos_human_haplotype)
 ## Reference switching
 
 An individual variation can be mapped to a new reference sequence given an
-alignment between the new and old references using the [`translate`](@ref).
+alignment between the new and old references using the
+[`translate`](@ref translate(::Variation{S,T}, ::PairwiseAlignment{S,S}) where {S,T})
+function.
 
 ```@repl call_variants
 ovis_human_alignment =
     PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), ovine)
 human_variation = first(variations(bos_ovis_haplotype))
 reference(ans) == bovine
-SequenceVariation.translate(human_variation, ovis_human_haplotype)
+SequenceVariation.translate(human_variation, ovis_human_alignment)
 reference(ans) == bovine
 ```