From a79b3aca716922e4ac526b92bf872ee7f51e611b Mon Sep 17 00:00:00 2001
From: Mikael Salson <mikael.salson@univ-lille1.fr>
Date: Thu, 5 Jul 2018 12:33:21 +0200
Subject: [PATCH] tools.js: get_mutations: deal with common gaps

As get_codons may return codons with gaps inside, testing for the codon length is not enough
we must first clean the codons by removing the common gaps.
However the codons must not be cleaned to early so that positions are properly counted.

See #2056
---
 browser/js/tools.js | 31 ++++++++++++++++++++++++-------
 1 file changed, 24 insertions(+), 7 deletions(-)

diff --git a/browser/js/tools.js b/browser/js/tools.js
index 75d679ef3..0f2d48321 100644
--- a/browser/js/tools.js
+++ b/browser/js/tools.js
@@ -97,14 +97,31 @@ function get_mutations(ref, seq, frame) {
                     mutations[nb_pos] = INS;
                 } else if (codons.seq[i][p] == '-') {
                     mutations[nb_pos] = DEL;
-                } else if (codons.seq[i].length == 3 &&
-                           codons.ref[i].length == 3 &&
-                           frame != undefined &&
-                           tableAA.hasOwnProperty(codons.seq[i]) &&
-                           tableAA[codons.seq[i]] == tableAA[codons.ref[i]]) {
-                    mutations[nb_pos] = SILENT;
                 } else {
-                    mutations[nb_pos] = SUBST;
+                    var codon1 = codons.ref[i];
+                    var codon2 = codons.seq[i];
+                    if (codon1.length > 3 && codon1.length == codon2.length) {
+                        codon1 = '';
+                        codon2 = '';
+                        // We may have common gaps (due to alignment with
+                        // other sequences) that need to be ignored
+                        for (var j = 0; j < codons.ref[i].length; j++) {
+                            if (codons.ref[i][j] != codons.seq[i][j] ||
+                                codons.ref[i][j] != '-') {
+                                codon1 += codons.ref[i][j];
+                                codon2 += codons.seq[i][j];
+                            }
+                        }
+                    }
+                    if (codon1.length == 3 &&
+                        codon2.length == 3 &&
+                        frame != undefined &&
+                        tableAA.hasOwnProperty(codon2) &&
+                        tableAA[codon1] == tableAA[codon2]) {
+                        mutations[nb_pos] = SILENT;
+                    } else {
+                        mutations[nb_pos] = SUBST;
+                    }
                 }
             }
             nb_pos++;
-- 
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