Fixed issue #254

ChangeLog

@@ -1,5 +1,10 @@
 Version 0.35.4
-  * Critical bug fix for crashes during output creation when -j is >1
+  * Bug fix for incorrect "Plots could not be created" message in HTML pages when -j is >1.
+  * Bug fix for #254: "Provided translation table #0 does not have 64 codons". This was a rare
+    case where two SNPs occur in the same codon of a CDS and also overlap a noncoding gene.
+
+Version 0.35.4
+  * Critical bug fix for crashes during output creation when -j is >1.
 
 Version 0.35.3
   * Fixed problem where HTML coverage and alignment files were not produced. (Bug introduced in v0.35.2)

configure.ac

@@ -19,7 +19,7 @@
 #                                               -*- Autoconf -*-
 # Process this file with autoconf to produce a configure script.
 AC_PREREQ([2.65])
-AC_INIT([breseq], [0.35.4], [[email protected]], [breseq], [http://barricklab.org/breseq])
+AC_INIT([breseq], [0.35.5], [[email protected]], [breseq], [http://barricklab.org/breseq])
 AC_CONFIG_AUX_DIR(aux_build)
 AC_CONFIG_MACRO_DIR([aux_build/m4])
 AC_CONFIG_HEADERS([aux_build/config.h])

src/c/breseq/reference_sequence.cpp

@@ -2726,7 +2726,7 @@ char cReferenceSequences::translate_codon(string seq, uint32_t translation_table
     ? cReferenceSequences::initiation_codon_translation_tables[translation_table]
     : cReferenceSequences::translation_tables[translation_table]
   ;
-  ASSERT(tt.size() == 64, "Provided translation table #" + to_string(translation_table) + " does not have 64 codons." + (gene.size()>0 ? " for gene " + gene :"") + ".");
+  ASSERT(tt.size() == 64, "Provided translation table #" + to_string(translation_table) + " does not have 64 codons" + (gene.size()>0 ? " for gene " + gene :"") + ".");
 
   return (cReferenceSequences::codon_to_aa_index.count(seq) == 0) 
     ? '?' 
@@ -2736,7 +2736,7 @@ char cReferenceSequences::translate_codon(string seq, uint32_t translation_table
 char cReferenceSequences::translate_codon(string seq, string translation_table, string translation_table_1, uint32_t codon_number_1, const string& gene)
 {  
   ASSERT(seq.size()==3, "Attempt to translate codon without three bases" + (gene.size()>0 ? " in gene " + gene :"") + ".");
-  ASSERT(translation_table.size()==64, "Provided translation table #" + to_string(translation_table) + " does not have 64 codons." + (gene.size()>0 ? " for gene " + gene :"") + ".");
+  ASSERT(translation_table.size()==64, "Provided translation table #" + to_string(translation_table) + " does not have 64 codons" + (gene.size()>0 ? " for gene " + gene :"") + ".");
   const string& tt = (codon_number_1 == 1) ? translation_table_1 : translation_table;
 
   return (cReferenceSequences::codon_to_aa_index.count(seq) == 0) 
@@ -3683,12 +3683,19 @@ void cReferenceSequences::annotate_mutations(cGenomeDiff& gd, bool only_muts, bo
             vector<string> codon_new_seq_list_j = split((*snp_muts[on_key][j])["codon_new_seq"], multiple_separator);
             vector<string> aa_new_seq_list_i = split((*snp_muts[on_key][i])["aa_new_seq"], multiple_separator);
             vector<string> aa_new_seq_list_j = split((*snp_muts[on_key][j])["aa_new_seq"], multiple_separator);
-
-            codon_new_seq_list_i[ii] = new_codon;
-            codon_new_seq_list_j[jj] = new_codon;
-            aa_new_seq_list_i[ii] =  translate_codon(new_codon, from_string((*snp_muts[on_key][i])["transl_table"]), from_string((*snp_muts[on_key][i])["aa_position"]));
-            aa_new_seq_list_j[jj] =  translate_codon(new_codon, from_string((*snp_muts[on_key][j])["transl_table"]), from_string((*snp_muts[on_key][j])["aa_position"]));
 
+            // If translation table is NA, then we don't translate for that gene!
+            vector<string> transl_table_list_i = split((*snp_muts[on_key][i])["transl_table"], multiple_separator);
+            vector<string> transl_table_list_j = split((*snp_muts[on_key][i])["transl_table"], multiple_separator);
+
+            if (transl_table_list_i[ii] != "NA") {
+              codon_new_seq_list_i[ii] = new_codon;
+              aa_new_seq_list_i[ii] =  translate_codon(new_codon, from_string(transl_table_list_i[ii]), from_string((*snp_muts[on_key][i])["aa_position"]));
+            }
+            if (transl_table_list_i[jj] != "NA") {
+              codon_new_seq_list_j[jj] = new_codon;
+              aa_new_seq_list_j[jj] =  translate_codon(new_codon, from_string(transl_table_list_i[jj]), from_string((*snp_muts[on_key][j])["aa_position"]));
+            }
             (*snp_muts[on_key][i])["codon_new_seq"] = join(codon_new_seq_list_i, multiple_separator);
             (*snp_muts[on_key][j])["codon_new_seq"] = join(codon_new_seq_list_j, multiple_separator);
             (*snp_muts[on_key][i])["aa_new_seq"] = join(aa_new_seq_list_i, multiple_separator);