update

biocpp · Feb 10, 2022 · 84a8f15 · 84a8f15
1 parent ddb17ba
commit 84a8f15
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Showing 6 changed files with 241 additions and 452 deletions.
diff --git a/include/bio/format/sam_input_handler.hpp b/include/bio/format/sam_input_handler.hpp
@@ -190,7 +190,8 @@ class format_input_handler<sam> : public format_input_handler_base<format_input_
 
                 ptr = res.ptr + 1; // skip cigar operation character
 
-                cigar_vector.emplace_back(cigar_count, seqan3::cigar::operation{}.assign_char(*res.ptr));
+                cigar_vector.emplace_back(cigar_count,
+                                          seqan3::assign_char_strictly_to(*res.ptr, seqan3::cigar::operation{}));
             }
         }
     }

diff --git a/include/bio/map_io/header.hpp b/include/bio/map_io/header.hpp
@@ -414,7 +414,9 @@ void header::read(std::string_view header_string)
                         {
                             sequence_length_was_present = true;
                             ++it; // skip :
-                            std::from_chars(&(*it), &(header_string.back()), get<0>(info));
+                            auto res = std::from_chars(&(*it), &(header_string.back()), get<0>(info));
+                            if (res.ec != std::errc{})
+                                throw format_error{"LN tag could not be parsed correctly."};
                             skip_until(seqan3::is_char<'\t'> || seqan3::is_char<'\n'>);
                             break;
                         }

diff --git a/include/bio/map_io/sam_tag_dictionary.hpp b/include/bio/map_io/sam_tag_dictionary.hpp
@@ -421,7 +421,7 @@ class sam_tag_dictionary : public std::map<uint16_t, detail::sam_tag_variant>
             }
             case 'Z' : // string
             {
-                (*this)[tag] = std::string{tag_value.data()};
+                (*this)[tag] = std::string(tag_value.begin(), tag_value.end());
                 break;
             }
             case 'H' :