From 48ae9fe9b6a3943ae7472e6196e9887c1fbb3985 Mon Sep 17 00:00:00 2001
From: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
Date: Thu, 22 Jun 2023 15:19:44 +0200
Subject: [PATCH] Error when translating gaps

DNA_Gap cannot be meaningfully translated, as it does not correspond to any
nucleotides, not even an unknown one. In fact, it's dubious that it's even a
nucleotide at all.
This PR makes `translate(!)` error when run on sequences with gaps, whereas
before this PR this was undefined behaviour (out-of-bounds access).
Alternative solutions could be to silently skip gaps, which is biologically
meaningful, but might lead to strange errors, or to insert AA_Gap, which can
only be done if the gaps come in groups of three corresponding to a whole
gap codon.
In the future we could change behaviour to skip gaps.

See issue 277
---
 Project.toml        |  2 +-
 src/geneticcode.jl  | 10 ++++++----
 test/translation.jl |  7 ++++++-
 3 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/Project.toml b/Project.toml
index 4976b65e..1851fa5e 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "BioSequences"
 uuid = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 authors = ["Sabrina Jaye Ward <sabrinajward@protonmail.com>", "Jakob Nissen <jakobnybonissen@gmail.com>"]
-version = "3.1.4"
+version = "3.1.5"
 
 [deps]
 BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
diff --git a/src/geneticcode.jl b/src/geneticcode.jl
index 6b67538c..7fab9d42 100644
--- a/src/geneticcode.jl
+++ b/src/geneticcode.jl
@@ -372,7 +372,11 @@ function translate!(aaseq::LongAA,
         a = reinterpret(RNA, ntseq[3i-2])
         b = reinterpret(RNA, ntseq[3i-1])
         c = reinterpret(RNA, ntseq[3i])
-        if isambiguous(a) | isambiguous(b) | isambiguous(c)
+        if isgap(a) | isgap(b) | isgap(c)
+            error("Cannot translate nucleotide sequences with gaps.")
+        elseif iscertain(a) & iscertain(b) & iscertain(c)
+            aaseq[i] = code[unambiguous_codon(a, b, c)]
+        else
             aa = try_translate_ambiguous_codon(code, a, b, c)
             if aa === nothing
                 if allow_ambiguous_codons
@@ -382,8 +386,6 @@ function translate!(aaseq::LongAA,
                 end
             end
             aaseq[i] = aa
-        else
-            aaseq[i] = code[unambiguous_codon(a, b, c)]
         end
     end
     alternative_start && !isempty(aaseq) && (@inbounds aaseq[1] = AA_M)
@@ -421,4 +423,4 @@ function try_translate_ambiguous_codon(code::GeneticCode,
         end
     end
     return found
-end
\ No newline at end of file
+end
diff --git a/test/translation.jl b/test/translation.jl
index a10ac5ac..fcf71a97 100644
--- a/test/translation.jl
+++ b/test/translation.jl
@@ -75,6 +75,11 @@
     # can't translate N
     @test_throws Exception translate(rna"ACGUACGNU", allow_ambiguous_codons=false)
 
+    # Can't translate gaps
+    @test_throws Exception translate(dna"A-G")
+    @test_throws Exception translate(dna"---")
+    @test_throws Exception translate(dna"AACGAT-A-")
+
     # issue #133
     @test translate(rna"GAN") == aa"X"
-end
\ No newline at end of file
+end