reader

Author: smehringer

include/bio/map_io/reader.hpp

@@ -8,16 +8,15 @@
 
 /*!\file
  * \brief Provides bio::map_io::reader.
- * \author Hannes Hauswedell <hannes.hauswedell AT decode.is>
+ * \author Svenja Mehringer <svenja.mehringer AT fu-berlin.de>
  */
 
 #pragma once
 
 #include <filesystem>
 
 #include <bio/detail/reader_base.hpp>
-// #include <bio/format/bcf_input_handler.hpp>
-// #include <bio/format/vcf_input_handler.hpp>
+#include <bio/format/sam_input_handler.hpp>
 #include <bio/map_io/header.hpp>
 #include <bio/map_io/reader_options.hpp>
 
@@ -28,13 +27,15 @@ namespace bio::map_io
 // reader
 // ----------------------------------------------------------------------------
 
-/*!\brief A class for reading sam files, namely SAM, BAM.
+/*!\brief A class for reading sam files, SAM, BAM.
  * \tparam options_t A specialisation of bio::map_io::reader_options.
  * \ingroup map_io
  *
  * \details
  *
  * TODO
+ *
+ * For more advanced options, see bio::map_io::reader_options.
  */
 template <typename... option_args_t>
 class reader : public reader_base<reader_options<option_args_t...>>
@@ -73,21 +74,21 @@ class reader : public reader_base<reader_options<option_args_t...>>
     // clang-format off
     //!\copydoc bio::reader_base::reader_base(std::istream & str, format_type const & fmt, options_t const & opt = options_t{})
     // clang-format on
-    reader(std::istream &                           stream,
+    reader(std::istream &                           str,
            format_type const &                      fmt,
            reader_options<option_args_t...> const & opt = reader_options<option_args_t...>{}) :
-      base_t{stream, fmt, opt}
+      base_t{str, fmt, opt}
     {}
 
     //!\overload
     template <movable_istream temporary_stream_t>
         //!\cond REQ
         requires(!std::is_lvalue_reference_v<temporary_stream_t>)
     //!\endcond
-    reader(temporary_stream_t &&                    stream,
+    reader(temporary_stream_t &&                    str,
            format_type const &                      fmt,
            reader_options<option_args_t...> const & opt = reader_options<option_args_t...>{}) :
-      base_t{std::move(stream), fmt, opt}
+      base_t{std::move(str), fmt, opt}
     {}
 
     //!\brief Access the header.

test/unit/format/sam_file_format_test_template.hpp

@@ -299,7 +299,6 @@ TYPED_TEST_P(sam_file_read, warning_rnext_not_in_header)
 //     EXPECT_THROW((fin.begin()), seqan3::format_error);
 // }
 
-
 // // ----------------------------------------------------------------------------
 // // sam_file_write
 // // ----------------------------------------------------------------------------