more work

Author: smehringer

include/bio/format/sam_input_handler.hpp

@@ -132,14 +132,27 @@ class format_input_handler<sam> : public format_input_handler_base<format_input_
     /* POS, MAPQ are handled correctly by default, unless we want pos to be read into an std:optional */
 
     //!\brief Overload for parsing CIGAR.
-    void parse_field(vtag_t<field::cigar> const & /**/, std::vector<seqan3::cigar> & parsed_field)
+    void parse_field(vtag_t<field::cigar> const & /**/, std::vector<seqan3::cigar> & cigar_vector)
     {
         std::string_view raw_field = get<field::cigar>(raw_record);
 
         if (raw_field != ".")
         {
-            size_t ref_length, seq_length; // used to construct the seqan3::field::alignment
-            std::tie(parsed_field, ref_length, seq_length) = seqan3::detail::parse_cigar(raw_field);
+            uint32_t cigar_count{};
+            char const * ptr = raw_field.data();
+            char const * end = ptr + raw_field.size();
+
+            while (ptr < end)
+            {
+                auto const res = std::from_chars(ptr, end, cigar_count); // reads number up to next chatacter
+
+                if (res.ec != std::errc{}) // parse number
+                    throw format_error{"Corrupted cigar string encountered"}; // todo, how in b.i.o?
+
+                ptr = res.ptr + 1; // skip cigar operation character
+
+                cigar_vector.emplace_back(cigar_count, seqan3::cigar::operation{}.assign_char(*res.ptr));
+            }
         }
     }
 
@@ -190,8 +203,9 @@ class format_input_handler<sam> : public format_input_handler_base<format_input_
     format_input_handler & operator=(format_input_handler &&) = default;
 
     template <typename options_t>
-    format_input_handler(std::istream & str, options_t const & options) : base_t{str}, file_it{str, false /*no_init!*/}
-
+    format_input_handler(std::istream & str, options_t const & options) :
+        base_t{str},
+        file_it{str, false /*no_init!*/}
     {
         // extract options
         if constexpr (requires { (bool)options.print_warnings; })
@@ -207,7 +221,7 @@ class format_input_handler<sam> : public format_input_handler_base<format_input_
             header_string += file_it->line;
             header_string += "\n";
         }
-        // header = map_io::header<std::vector<std::string>>{std::move(header_string)};
+        header = map_io::header<std::vector<std::string>>{std::move(header_string)};
     }
 
     auto const & get_header() const { return header; }